Single molecule nucleic acid nanoparticles

ABSTRACT

The present technology relates to a nanoparticle platform based on the unique and varied properties of DNA. Circular DNA can be replicated using a strand displacing polymerase to generate long linear concatamers of controllable length that spontaneously fold into a ball conformation due to internal base-pairing. These balls of DNA are discreet particles that can be made in variable sizes on a nanometer size scale in a scalable manner. The particles can be used in a variety of manners, discussed herein, including specific targeting, drug delivery to cancer cells, and diagnostics. Nanoparticles may also serve as multifunctional platforms for the integration of many currently used cancer therapeutic techniques.

RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.13/502,729 filed Jun. 28, 2012 which is the U.S. National Phase ofInternational Application No. PCT/US 2010/053270 entitled “SINGLEMOLECULE NUCLEIC ACID NANOPARTICLES”, filed Oct. 19, 2010 and publishedin English on Apr. 28, 2011 as WO 2011/050000, which claims priority toU.S. Provisional Application No. 61/279,408 filed on Oct. 20, 2009, thecontents of which are incorporated by reference in their entireties.

STATEMENT REGARDING FEDERALLY SPONSORED R&D

This invention was made with government support under NIH Grant/ContractNumbers U54CA119933501 and U54CA119335 awarded by the NationalInstitutes of Health of the United States of America. The government hascertain rights in the invention.

REFERENCE TO SEQUENCE LISTING

The present application is being filed along with a Sequence Listing inelectronic format. The Sequence Listing is provided as a file entitledUCSD025.TXT, created Oct. 19, 2010, which is approximately 3.2 KB insize. The information in the electronic format of the Sequence Listingis incorporated herein by reference in its entirety

FIELD OF THE INVENTION

The present technology relates to the fields of molecular biology,biochemistry, medicine, and cancer therapeutics. In particular, methodsand compositions for making and utilizing nanoparticles comprisingnucleic acids are provided.

BACKGROUND

DNA is one of the most thoroughly characterized molecules with regard tostructure, chemistry, and modification, and has the capability to servea wide variety of functions. It can be, and has been, used as a scaffoldfor the integration of varying entities due to its well defined abilityto base-pair hybridize. With the discovery of aptamers and therealization that DNA has the capability to structurally and chemicallyrecognize other molecules with near anti-body specificity at a fractionof the difficultly of synthesis, a new field of DNA based targetingmolecules was born. Today there are FDA approved therapeutics basedsolely on DNA, such as the VEGF aptamer.

Current nanoparticle-based approaches to treating cancer includeconstructs composed of polymer, silica, or gold nanoparticles,liposomes, and less frequently such platforms as carbon nanotubes andviral capsids. These structures are coated with a variety offunctionalizing entities such as polyethylene glycol (PEG) forbiocompatibility, various targeting peptides, antibodies, smallmolecules, or aptamers and some form of therapeutic.

SUMMARY

The present technology relates to a nanoparticle platform based on theunique and varied properties of DNA. Circular DNA can be replicatedusing a strand displacing polymerase to generate long linear concatamersof controllable length that spontaneously fold into a ball conformationdue to internal base-pairing. These balls of DNA are discreet particlesthat can be made in variable sizes on a nanometer size scale in ascalable manner. The particles can be used in a variety of manners,discussed herein, including specific targeting, drug delivery to cancercells, and diagnostics. Nanoparticles may also serve as multifunctionalplatforms for the integration of many currently used cancer therapeutictechniques.

Some embodiments described herein include methods of making ananoparticle including contacting a circular single-stranded nucleicacid template with a nucleic acid polymerase, wherein the nucleic acidtemplate encodes an aptamer; and amplifying said template with saidpolymerase to produce said nanoparticle, wherein said nanoparticlescomprises a concatemer of the sequence of said template. In suchembodiments, the nucleic acid template can be DNA or RNA. In moreembodiments, the nucleic acid polymerase is a strand displacingpolymerase, such as a DNA polymerase, and can be selected from the groupconsisting of phi29 polymerase, Klenow fragment, VENT® (Exo) DNApolymerase, 9° N_(m) DNA polymerase, Bst DNA polymerase, M-MuLV reversetranscriptase, and AMV reverse transcriptase. In some embodiments, theamplifying step has a duration of more than about 1, 5, 10, 25, 30, 50,and 120 minutes. Some methods of making a nanoparticle can also includecircularizing a linear nucleic acid template to produce the circularnucleic acid template. The linear nucleic acid template can be more than10, 50, 100, or 1000 bases in length.

Some embodiments described herein include a nanoparticle made accordingto the methods described herein. In such embodiments, the nanoparticlecan include DNA. The DNA can be more than 1 kb, 10 kb, 100 kb, 1 Mb, 10Mb, 100 Mb, and 500 Mb in length. The DNA can encode a sequence selectedfrom a siRNA, reporter gene, therapeutic protein, and CpG sequence. Someembodiments include nanoparticles containing a nucleic acidintercalating drug. Such drugs can include Doxorubicin, Daunorubicin,and Dactinomycin. More embodiments include nanoparticles containing anoligonucleotide-linked entity including an aptamer, drug, peptide, andsiRNA.

Some embodiments include liposomes containing nanoparticles. Moreembodiments include pharmaceutical compositions containingnanoparticles. Particular embodiments include methods of treating cancerincluding administering the pharmaceutical compositions described hereinto a subject in need thereof. Even more embodiments include kitscontaining the pharmaceutical compositions described herein andinstructions for use of the kit.

Some embodiments include methods for identifying nanoparticlescontaining aptamers including generating a library of nanoparticlescomprising putative aptamers; and screening the library. The screeningcan include contacting the library to a capture probe; and selecting fora nanoparticle that binds the capture probe. The capture probe caninclude a tumor cell.

Some embodiments include nanoparticles containing a single-strandnucleic acid including a concatemeric sequence encoding an aptamer. Insome embodiments, the nanoparticle can include DNA. For example, the DNAcan be more than 1 kb, 10 kb, 100 kb, 1 Mb, 10 Mb, 100 Mb, and 500 Mb inlength. The DNA can encode a sequence selected from a siRNA, reportergene, therapeutic protein, and CpG sequence. Some embodiments includenanoparticles containing a nucleic acid intercalating a drug. Such drugscan include Doxorubicin, Daunorubicin, and Dactinomycin. Moreembodiments include nanoparticles containing an oligonucleotide-linkedentity including an aptamer, drug, peptide, and siRNA.

Some embodiments include methods to identify tumor cells. Such methodscan include contacting a tumor cell with a nanoparticle in which theaptamer selectively binds to the cell; and identifying binding of theaptamer to the cell. More embodiments include the identifying binding ofthe aptamer to the cell to include identifying a reporter moietyassociated with the nanoparticle. The reporter moiety can include aradioactive probe, a reporter protein, a reporter gene, and afluorescent molecule.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A shows a schematic diagram for uses of DNA nanoparticles.

FIG. 1B shows a schematic overview of DNA nanoparticle synthesis andmodular DNA particle library creation. Single module libraries can bebiopanned, whereas the modules within the multimodule libraries can bere-assorted from round to round, creating particles with novelcombinations of modules.

FIG. 2 relates to a visualization of DNA nanoparticles. Panel A shows aphotomicrograph of DNA nanoparticles produced by a 30 minute RCAreaction. The particles were labeled after synthesis with Sybr Green dyeand imaged at 100× in a fluorescent microscope. Panel B shows a graph ofsorted DNA-NP. DNA nanoparticles were made by RCA reactions of varyingtimes, labeled with Oligreen dye, and run on a flow cytometer. Thefluorescence intensity correlates with the size of the particlesconsequent to the reaction time. (Graph a: unlabeled beads; graph b: 7.5min DNA-NP; graph c: 30 min DNA-NP; graph d: 60 min DNA-NP). Panel Cshows a graph relating to DNA nanoparticles produced with Alexa488labeled nucleotides and run on a flow cytometer. Panel D shows a graphrelating to unlabelled DNA nanoparticles hybridized with a complementaryoligonucleotide probe labeled with Alexa-647.

FIG. 3 relates to DNA nanoparticles sized by Dynamic Light Scattering(DLS). Panel A provides DLS data showing increasing size with RCAreaction time. The particles rapidly (10 minutes) obtain a mean size of˜200 nm. After one hour they are ˜300 nm. Panel B demonstratesmonoexponential autocorrelation decays indicating significantmonodispersity. All data was collected on a Zetasizer Nano-ZS.

FIG. 4 shows a schematic of the flow of selection scheme for DNAnanoparticles that bind human dendritic cells. A 100 base library with a60 base random region flanked by 2 20 base primer sites is ligated andamplified with Rolling Circle Amplification to produce nanoparticles.The nanoparticles are incubated with the target cells and washed.Remaining nanoparticles are amplified by PCR and then asymmetrically PCR(using only one primer) to generate an excess of the desired strand. Thedesired strand is re-ligated and the cycle is repeated.

FIG. 5 shows a graph of fluorescence and indicates the selection of DNAnanoparticles that bind to human dendritic cells (DCs). The pool of DNAnanoparticles after 7 rounds of selection was regenerated withfluorescent nucleotides and compared to a similarly labeled non-specificcontrol DNA nanoparticle. The red curve shows DCs with free labelednucleotides. There is a clear shift in the labeling intensity with theselected particles.

FIG. 6 provides flow cytometry data for 5 positive clones sequenced fromround 7 of selection protocol. Controls included a DNA nanoparticle thatdid not bind (N05), dendritic cells alone and dendritic cells with freeAlexa488-dCTP used to label the DNA.

FIG. 7 relates to a DNA nanoparticle selection process.

FIG. 8 relates to an embodiment that includes library generation,ligation, and RCA.

FIG. 9 relates to an embodiment that includes PCR amplification andasymmetric PCR.

FIG. 10 relates to an embodiment that includes multimodule particlecreation from single module libraries.

FIG. 11 relates to an embodiment that includes non-modular PCRamplification of multimodule particles to preserve module combinations.

FIG. 12 relates to an embodiment that includes subtractive screening. Anirrelevant cell line is used to absorb non-specific cell bindingparticles.

FIG. 13 relates to two methods of introducing paramagnetic properties tothe DNA nanoparticles via iron oxide-oligonucleotide conjugates.

FIG. 14 relates to an embodiment of DNA-NP synthesis by rolling circleamplification.

FIG. 15 provides data relating to RCA reaction kinetics. Upper panel: 1nM ligated oligonucleotides were used as a template for phi29 polymeraseto perform RCA and produce single stranded particles. Lower panel:incorporation of phosphorothioate nucleotide. The rate of an RCAreaction was monitored by oligreen fluorescence. Reactions containeddATP, dGTP, dTTP, and either dCTP, a 50:50 mixture of dCTP and2′-deoxycytidine a-thiotriphosphate, or only 2′-deoxycytidinea-thiotriphosphate. The reaction proceeds 50% slower when only modifiednucleotides are used for that one base.

FIG. 16 provides data relating to a visualization of DNA nanoparticles.Panel A shows a photomicrograph of DNA nanoparticles produced by a 30minute RCA reaction. The particles were labeled after synthesis withSybr Green dye and imaged at 100× in a fluorescent microscope. Panel Brelates to DNA nanoparticles that were made by RCA reactions of varyingtimes, labeled with Oligreen dye, and run on a flow cytometer. Thefluorescence intensity correlates with the size of the particlesconsequent to the reaction time. Panel C shows a WETSEM image of DNA-NPproduced from a 30 min reaction. The particles are imaged while bound toa poly-lysine coated membrane in aqueous solution.

FIG. 17 relates to DNA nanoparticles sized by Dynamic Light Scattering(DLS). Panel A provides DLS data showing increasing size with RCAreaction time. The particles rapidly (10 minutes) obtain a mean size of˜200 nm. After one hour they are ˜300 nm. Panel B provides data showingmonoexponential autocorrelation decays indicating significantmonodispersity. All data was collected on a Zetasizer Nano-ZS.

FIG. 18 relates to the specificity of DC binding clone 3. Particles werelabeled and tested as described herein.

FIG. 19 provides data relating to specific binding and uptake of Clone 3by DC. Panel A relates to Clone 3 DNA-NP synthesized with alexa488nucleotides and incubated with DC and cell lines P815 (mousemastocytome) and THP1 (human acute monocytic leukemia). Flow cytometrywas performed with clone 3, it's reverse complement particle, and DCsincubated with just the nucleotide mix. The same samples were assessedby fluorescent microscopy. The incubations were done on ice. Panel Brelates to DC incubated with clone 3 particles at 37° C. No fluorescencewas seen in P815 or THP1 incubated with clone 3, nor was any observed inDC incubated with the control reverse complement particle (not shown).

FIG. 20 provides data relating to clone 3 DC binding DNA-NP elicitscytokine secretion and Ca²⁺ flux. Panel A relates to DCs exposed toDC-binding DNA-NPs (DNA(+)) or control DNA-NPs that do not bind to DCs(DNA(−)), LPS, or media control for 48 h and the amount of II-6 secretedinto the cell culture supernatants was determined by ELISA. DC bindingDNA-NP elicited the most IL-6 production. Panel B relates to Ca²⁺ fluxfollowed in real time after exposure of the cells to either clone 3 (toppanel) or the control (bottom panel) DNA-NP. The FLIPR Calcium 5 assaywas used in conjunction with the FlexStation 3 scanning plate reader,both from Molecular Devices. DC binding nanoparticles that have beenpurified by dialysis into cell culture grade PBS are added to cell/dyesuspensions in a 96 well plate and fluorescent readings are monitoredcontinuously for approximately 150 seconds following administration ofnanoparticles. Fluorescent signals indicate increased concentrations ofintracellular calcium that is released upon stimulation by DNAnanoparticles.

FIG. 21 relates to hybrid DNA nanoparticle formation. Templates for twoparticles can be fused by ligation. One ligation primer is dideoxyterminated so that it can not prime the RCA. The resulting DNA-NPcontains many copies of each sequence, at a precise 1:1 ratio. Ifdesired the ratio could be tuned by altering the number of copies of oneor the other in the template construction.

FIG. 22 provides data relating to 10⁵ immature human DCs generated fromHLA.A2. Positive donors were cultured in the presence of Hp-91 or acontrol peptide Hp-46 (200 μg/mL), or left untreated (medium) for 48 h.DCs were washed and cultured with the melanoma peptide gp100 (500 ng/ml)and gp100-specific responder cells at a DC to responder ratio of 1:2overnight. The number of IFN-γ□ secreting cells was determined 24 hlater. The plate was scanned and the spots were counted automaticallyusing the image analysis system ELISPOT reader. The data shown is thenumber of IFN-γ-spot-forming cells/well, are means (+/−SEM) of twoindependent experiments using DCs from different donors.

FIG. 23 provides data relating to Hp-91(270 μg), pI:C (125 μg), orPam3Cys (125 μg) injected into B16 melanoma and the mice were sacrificed24 h after the injection. The tumor was embedded in OCT and frozensections were stained for Mac 1 (macrophages), CD11c (DCs), and CD3 (Tcells) by immuno-histochemistry. Pictures were taken in brightfield at20×. Higher doses of pI:C and Pam3Cys (500 μg) still showed no T celland DC recruitment (data not shown).

FIG. 24 relates to embodiments that include a strategy for selection andcombinatorial breeding of multimeric polyvalent DNA nanoparticles.Step 1. Several libraries with unique ligation and PCR primers aregenerated. Step 2. Each library is independently screened for a fewrounds against the target to create an initial enriched pool. Step 3.The products of the initial screenings are combinatorially assembledinto multimeric templates and polyvalent DNA particles are generated.Step 4. The particles are subjected to subtractive screening to enrichthe desired binding activity and eliminate unwanted crossreactivities asdescribed herein. In each selection step the individual librarycomponents are re-assorted, creating additional combinatorial diversityfrom which optimal particles can be selected.

FIG. 25 shows a photograph of DNA nanoparticles made with reaction timesof 5 and 30 minutes, respectively.

FIG. 26 shows flow cytometry data illustrating increasing fluorescencewith increasing reaction time indicating larger particles.

FIG. 27 shows a spectrograph of Doxorubicin and Doxorubicin with DNAnanoparticles. Doxorubicin is titrated into ˜500 ng DNA nanoparticlesand the fluorescence is quenched as binds. At low Doxorubicinconcentrations nearly all fluorescence is quenched. With increasingconcentration of Doxorubicin, the DNA nanoparticles become saturated andfree Doxorubicin in solution can fluoresce.

FIG. 28 shows a schematic diagram of an example library templateoligonucleotide.

FIG. 29 relates to library generation and screening. Panel A shows aschematic diagram of some embodiments that include of a librarygeneration strategy. Panel B shows a schematic of a screening strategyfor use on touch preparations of primary tumor samples. Panel C shows aschematic of an amplification and regeneration method for repeatedscreenings and enrichment of target binders.

FIG. 30 shows a schematic for an example strategy for selection andcombinatorial breeding of multimeric polyvalent aptamer particles. Step1 shows several aptamer libraries with unique ligation and PCR primersare generated. Step 2 shows each library is independently screened forseveral rounds against the target. Step 3 shows the products of theinitial screenings are combinatorially assembled into multimerictemplates and polyvalent DNA particles are generated. Step 4 shows theparticles are subjected to subtractive screening to enrich the desiredbinding activity and eliminate unwanted crossreactivities.

FIG. 31 shows a graph of fluorescence over time. RCA reactions were runusing either dNTPs, a mixture of dNTP and phosphorothioate backbonecytosine nucleotides (CαSTP) at a 1:1 ratio with dCTP, or with anucleotide cocktail where all dCTP was replaced with CαSTP.

FIG. 32 shows graphs of spectrometer readings vs. drop count.

FIG. 33 shows graphs of DNA recovery from drop analysis, and dialysis ofnucleotides from DNA on Millipore MF membranes.

FIG. 35 shows a graph of cleaning of RCA with centricon YM-30 atdifferent speeds.

FIG. 36 shows a graph of digestion of RCA products and single strandedpadlock probes with Exonuclease I and RecJf.

FIG. 37 shows a graph of fluorescence intensity for various DNAparticles.

FIG. 38 shows DNA nanoparticles visualized with Sybr Green dye. Lowerpanel: 100× of 30 min RCA. Upper panel: 100×90 min RCA. Particle densityis dependent on the spot and the time it has been under the light(photo-bleaching occurs).

FIG. 39 shows a graph of incorporated Alexa 488 fluorescence.

FIG. 40 shows a graph of hybridized probe fluorescence.

FIG. 41 shows a graph of size distribution by intensity.

FIG. 42 shows a photograph of an agarose gel.

FIG. 43A shows graphs of fluorescence intensity, and includes an exampleof a cloned particle (shaded) with high affinity for DC as compared to acontrol particle (red) or unstained cells (blue and grey).

FIG. 43B shows a graph of fluorescence intensity, and includes anexample of clonal particle was assayed against the MDA-MB-231 breastcancer cell line.

FIG. 44 shows a graph of fluorescence of particles loaded withdoxorubicin.

FIG. 45 shows a graph of OD490 over time.

FIG. 46 shows a graph of IgM secreted from PBMC in the presence ofnanoparticles.

FIG. 47 relates to production and basic characterization of DNAnanoparticles. Panel A relates to DNA nanoparticles are produced bycircularizing a 100 nM concentration of a 94 base ssDNA template with T4Ligase and a 300 nM concentration of a 31 base templating primer.Polymerization was done with phi29 DNA polymerase at 30° C. for 30minutes and terminated with EDTA. Discrete particles are stained withSYBR Green and viewed under a 100× oil objective. Panel B: Nanoparticlescreated for various reaction times are measured with Dynamic LightScattering to validate size and demonstrate positive correlation ofhydrodynamic radius with reaction time.

FIG. 48 and FIG. 49 relate to flow cytometry assays of DNA nanoparticlesincorporating Alexa488 dCTP. Nine rounds of selection were performed assummarized in FIG. 9 after which the selected population was used togenerate fluorescent DNA nanoparticles which were incubated againstdendritic cells. From the 9^(th) round of selection, individualpopulation members were cloned using a Promega pGEM-T cloning kit andserved as templates for fluorescent nanoparticle generation which wereindividually incubated with dendritic cells. Of these clones, severalwere observed to bind DCs with varying degrees of efficacy. Thevariation can be seen in FIG. 49 which compares several “positive”clones to a “negative” clone with less binding capability. FIG. 48provides data relating to a comparison of the 9^(th) round selectionpopulation with the whole and negative control. In this case, it wasobserved that the population exhibited a net shift over an individualmember indicating that, while not complete, the selection had enrichedfor nanoparticles with enhanced binding capabilities. It is important tonote that the incorporation efficiency of Alexa488 OBEA-dCTPs by phi29polymerase was calculated to be only ˜1.5%. While it did not appear tosignificantly slow the reaction, the poor incorporation is likely thecause of the smaller shifts in the flow peaks.

FIG. 50 provides data relating to flow cytometry data and brightfield/fluorescence microscopy for cell binding assays of dendritic cellbinding DNA nanoparticles. Microscopy images show bright field,fluorescent and overlays from left to right. For flow cytometry data,DNA nanoparticles of both the selected sequence (Clone 3, green) and itsreverse complement incorporating Alexa₄₈₈-dCTP were assayed for bindingto DCs, P815 and THP1 cell lines. DCs were cultured as described herein.0THP1 and P815 cells were maintained in RPMI supplemented with 10% FBSand 1% PSG at 37° C. Fluorescent DNA nanoparticles incubated with 5×10⁴cells of each respective cell line were aliquoted and resuspended in 50μL, of media (DCs resuspended in their original media). 50 μL, of theRCA reaction mix containing synthesized DNA nanoparticles was addeddirectly to each cell line, mixed gently, and incubated on ice for 20min in the dark. Cells were washed 3 times and formaldehyde fixed to beanalyzed by flow and microscopy. Both analyses clearly demonstrate DCspecificity as well as specificity for the selected sequence over itsreverse complement.

FIG. 51 relates to the generation of ssDNA nano-particles: ♦(upperline): cells+qPCR+RCA; ▪: cells+qPCR reagent; ▴: cells+qPCR+RCA(−);♦(lower line): cells. A graph of fluorescence (R) vs. number of cycles.Eight bio-panning cycles have been made starting from a randomDNA-library. In each bio-panning cycle, MDA-MB-231 cells (epithelialbreast cancer cells) were incubated with ssDNA nanoparticles and thebinding particles were amplified by qPCR. The goal of each cycle was toenrich and amplified the binding motifs.

FIG. 52 relates to DNA gel of amplified sequences: After eachbio-panning cycle, the amplified samples were run in a DNA gel where theamplified products can be visualized. In all the bio-panning cycles,amplified products were observed only from the samples corresponding tocells+RCA particles (lane 5). No amplification of cell DNA was observed(lane 2, 3 and 4). Line 1 represents the molecular weight ladder.

FIGS. 53A-53C show graphs including FACS analysis to test the bindingand specificity of ss-DNA nanoparticles. ss-DNA nanoparticles weregenerated by RCA and incubated with the epithelial breast cancer cells,MDA-MB-231.

FIGS. 54A-54C shows graphs including FACS analysis to test the bindingand specificity of ss-DNA nanoparticles. ss-DNA nanoparticles weregenerated by RCA and incubated with the epithelial breast cancer cells,MCF-7.

FIGS. 55A-55C show graphs including FACS analysis to test the bindingand specificity of ss-DNA nanoparticles. ss-DNA nanoparticles weregenerated by RCA and incubated with the monocytic cell line, THP-1.

FIG. 56 shows a general example scheme for the production bi-specificDNA-nanoparticles (NP) that bind to both tumor cells and T cells.

FIGS. 57A and 57B summarize the results of the selection of pancreaticcancer cell line panc02 targeting particles. The mouse pancreatic linespanc02 was panned with a single module DNA nanoparticle library. Afterthe 3^(rd) and 4^(th) round, the selected pool was fluorescently labeledand tested on the target cells by flow cytometry (FIG. 57A). The clonesthat contain the AATGGGGCG (SEQ ID NO:12) motif bind specifically topanc02, whereas the clones lacking the motif (C21 and C50) do not (FIG.57B). In the experiment shown, the four clones that show a fluorescentshift in the left panel all contain the motif whereas the clones withoutthe motif are no better than controls. No difference is seen againstother epithelial cell lines.

FIG. 58 provides data relating to an ELISA experiment. Mice immunizedwith DC binding DNA-NP, or CpG oligonucleotides (ODN).

DETAILED DESCRIPTION

Some embodiments of the present invention include nucleic acid basednanoparticles comprising multi-kilobase long concatamer copies of adefined aptameric sequence. These can display a sequence several hundredtimes throughout the particle, as well as on the surface of thenanoparticles. These nanoparticles have the advantage of a significantincrease in the strength of binding over current aptamer approaches.

Recent advancements in the understanding of immunity has brought tolight the immunological properties of certain sequences of DNA, such asCpG sequences, can greatly stimulate the immune system. CpG sequencescan be used as an adjuvant for the delivery of DNA based vaccines. A DNAbased nanoparticle can easily incorporate these sequences to bedisplayed hundreds of times on a single particle potentially increasingthe potency several orders of magnitude.

More embodiments include nanoparticles comprising small molecules, forexample, drugs such as chemotherapeutics. Many of the most common cancerchemotherapeutics are natural DNA binding molecules. Delivery ofchemotherapeutics bound to DNA is a method to sequester suchchemotherapeutics for transport to a delivery site. DNA is also easilymodified through altered base composition to control such parameters asdegradation, salt, and pH responsiveness.

More embodiments include nanoparticles comprising nucleic acid encodingsequence information. For example, DNA is an information carrier thatcould be utilized for applications such as gene therapy and siRNAdelivery. More embodiments can include DNA encoding therapeutic proteinsand reporter genes.

One major advantage of this approach includes the ability to avoidcomplex conjugation chemistries for targeting specificity,biocompatibility, and drug incorporation of nanoparticles. Also,clinical testing may be simpler for nucleic acid based nanoparticles.For example, whereas the addition of any addition to other types ofnanoparticles may create a new entity for clinical testing, here, asingle particle of DNA can incorporate many therapeutic functions andremains one type of molecule, namely, DNA, a molecule that has beenalready approved for in vivo human use.

DNA nanoparticles can be made cheaply in a volumetric scalable way withsimple techniques. Once validated for function and developed they wouldmost likely meet regulatory guidelines quickly and be translated intoclinical use. In addition to clinical use, DNA nanoparticles can be usedin diagnostics, for example, as sensing agents utilizing DNA's abilityto react to its microenvironment.

The basic creation of DNA nanoparticles begins with a padlock probe ofsingle stranded DNA. The sequence of this probe can be engineered for avariety of purposes, non-limiting examples can include, immunogenicstimulation, enzymatic degradation, and specific hybridization. Thisprobe can vary in length from at least about 2 bases, at least about 5bases, at least about 10 bases, at least about 50 bases, at least about100 bases, at least about 500 bases, at least about 750 bases, at leastabout 1000 bases, at least about 1 kb, at least about 5 kb, at leastabout 10 kb, at least about 50 kb, and longer.

First, the probe is ligated endwise to form a closed loop circle via atemplating primer complementary to the ends of the probe. The templatingprimer then serves as a primer for polymerization with a stranddisplacing polymerase with the circle acting as an endless template inRolling Circle Amplification (RCA) (FIG. 1A).

The polymerization can proceed for a period of time, after which acertain length of single stranded DNA is created comprising concatamerrepeats of the original padlock probe. The concatamer can spontaneouslyform a globular shape based on internal base pairing. The size of thenanoparticles can be controlled by, for example, the polymerization timeof the reaction, the type of polymerase used, and reaction conditionssuch as salt concentration and pH. In some embodiments, thepolymerization can proceed for a length of time according to the lengthof product desired, where a longer time can produce a longer product.

Non-limiting examples for functions of the nanoparticles are shown inFIG. 1A. The DNA nanoparticle has multiple copies of the originalsequence both internally base-paired as well as displayed on the surfacewhich can serve as hybridization sites for DNA conjugated entities or asa multivalent display of an aptameric sequence that can be used fortargeting. They might also be coded to contain immunostimulatorysequences such as certain CpG sequences. Furthermore, it may be possibleto encode genetic information in the RCA product and/or encase the DNAnanoparticles in other nanostructures such as liposomes.

Some embodiments include nanoparticles with aptamers for use in therapy.These particles have several advantages. For example, DNA is essentiallynon-toxic, biocompatible, and can used as a scaffold for the attachmentof other agents. Also, DNA particles can be easily loaded with DNAbinding chemotherapy agents, such as Doxorubicin and, if targeted by anaptamer sequence, may represent an ideal targeting mechanism for suchdrugs.

Chemically diverse libraries are a rich source of potential ligands forbiomolecules and cellular targets of interest. When modular biopolymerssuch as nucleic acids or polypeptides are used, the combinatorialdiversity of these libraries can become astronomical and well beyond thecapabilities of systemic high throughput screening methods. Combingthese libraries then requires iterative schemes that couple a selectionstep with an amplification step. For peptides, display of a givenpeptide on a bacteriophage, virus, or bacteria allows amplification bygrowth of the host organism (Scott J K, Smith G P. Searching for peptideligands with an epitope library. Science. 1990; 249: 386-390). Nucleicacids are typically amplified by some variation of PCR (Tuerk C, Gold L.Systematic evolution of ligands by exponential enrichment: RNA ligandsto bacteriophage T4 DNA polymerase. Science. 1990; 249: 505-510). Thesetools have been used to select peptides and short nucleic acid sequences(aptamers) that can bind to a wide variety of proteins and cellulartargets.

However, peptide and aptamer libraries have some distinct limitations.Many peptide display formats, such as phage, present many copies of eachpeptide per particle. This can allow the recovery of relatively lowaffinity interactions that benefit from the high avidity of thepresentation format. However, it may be difficult to maintain thedesired binding avidity and specificity when the selected peptides aremoved to another particle or molecule. Aptamer libraries can suffer fromthe reverse complication since they are usually presented in amonovalent format. Aptamers have been most clinically useful when a highaffinity interaction can function in an antagonist manner, though theyhave been used as targeting moieties attached to nanoparticle drugdelivery vehicles (Farokhzad O C, et al. Targeted nanoparticle-aptamerbioconjugates for cancer chemotherapy in vivo. Proc Natl Acad Sci USA.2006; 103:6315-6320; Bagalkot V, et al. An aptamer-doxorubicin physicalconjugate as a novel targeted drug-delivery platform. Angew Chem Int EdEngl. 2006; 45:8149-8152). However, when aptamers that were selected ina monovalent format are attached to particles in a multivalent way,specificity can be lost as low affinity interactions gain avidity. Inaddition, there is always a concern that the transfer or attachment of apeptide or aptamer to a new molecule or particle may alter itsconformation and binding affinity for the target of interest. Thus fortargeting moieties on particles, it would be ideal to select the optimalligand in the very context in which it will be used.

A methodology has been developed for the construction of large librariesof DNA nanoparticles and a process for the iterative selection ofparticles with the desired properties. When coupled with the otherstructural, functional, chemical, and informatic properties of DNA theseselectable particles allow the creation of multifunctional particles forbiomedical and therapeutic use.

Molecular Evolution

Specific molecular recognition is the basis for most of life'sbiological processes, but in the clinic and laboratory the tools forsuch are limited to monoclonal antibodies, peptides, aptamers, smallmolecules or natural biomolecule ligands. These tools have not matchedwell with the problem of specific recognition of neoplastic cells fromtheir normal counterparts for several reasons. The primary reason isthat unique molecular structures common to neoplastic cells of a giventype but distinct from normal cells are rare and all of the methodsabove, in their simple forms, target only a single molecular shape.Bi-specific or multi-specific versions have been described, for examplediabodies and bi-specific antibodies, but these are difficult to produceand not widely used (Kortt A A, et al. Dimeric and trimeric antibodies:high avidity scFvs for cancer targeting. Biomol Eng. 2001; 18:95-108).High affinity binding moieties can also suffer a loss of specificitywhen combined because already high affinity interactions do no benefitmuch from coupled or multi-valent interactions, but previously lowaffinity interactions can gain avidity and compromise selectivity.

Chemically diverse libraries are a rich source of potential ligands forbiomolecules and cellular targets of interest. When modular biopolymerssuch as nucleic acids or polypeptides are used, the combinatorialdiversity of these libraries can become astronomical and well beyond thecapabilities of systematic high throughput screening methods. Combingthese libraries requires iterative schemes that couple a selection stepwith an amplification step. For peptides, display of a given peptide ona bacteriophage, virus, or bacteria allows amplification by growth ofthe host organism (Scott J K, Smith G P. Searching for peptide ligandswith an epitope library. Science. 1990; 249:386-390). Nucleic acids aretypically amplified by some variation of PCR. Subtractive and in vivoselection schemes have been developed for aptamer and phage displayedpeptide libraries that can enhance the cell specificity of recoveredtargeting ligands. Cellular targeting has been demonstrated by librariesof peptides and oligonucleotide aptamers (Siegel D L, et al. Isolationof cell surface-specific human monoclonal antibodies using phage displayand magnetically-activated cell sorting: applications inimmunohematology. J Immunol Methods. 1997; 206:73-85; Rasmussen U B, etal. Tumor cell-targeting by phage-displayed peptides. Cancer Gene Ther.2002; 9:606-612; Hicke B J, et al. Tenascin-C aptamers are generatedusing tumor cells and purified protein. J Biol Chem. 2001;276:48644-48654).

However, peptide and aptamer libraries have some distinct limitations.Most peptide display formats, such as phage, present many copies of eachpeptide per particle. This can allow the recovery of relatively lowaffinity interactions that benefit from the high avidity of thepresentation format. However, it may be difficult to maintain thedesired binding avidity and specificity when the selected peptides aremoved to another particle or molecule. Aptamer libraries can suffer fromthe reverse complication since they are usually presented in amonovalent format. Aptamers have been most clinically useful when a highaffinity interaction can function in an antagonist manner, though theyhave been used as targeting moieties attached to nanoparticle drugdelivery vehicles (Farokhzad O C, et al. Targeted nanoparticle-aptamerbioconjugates for cancer chemotherapy in vivo. Proc Natl Acad Sci USA.2006; 103:6315-6320; Bagalkot V, et al. An aptamer-doxorubicin physicalconjugate as a novel targeted drug-delivery platform. Angew Chem Int EdEngl. 2006; 45:8149-8152). However, when aptamers that were selected ina monovalent format are attached to particles in a multivalent way,specificity can be lost as low affinity interactions gain avidity. Inaddition, there is always a concern that the transfer or attachment of apeptide or aptamer to a new molecule or particle may alter itsconformation and binding affinity for the target of interest. Thus fortargeting complex targets like cells where specificity is a greaterconcern than raw affinity, it would be ideal to select the optimalligand in the very context in which it will be used.

Furthermore, while aptamer and phage display technologies areoccasionally referred to as evolutionary processes (one of the earliestaptamer papers described the process as SELEX—Systematic Evolution ofLigands by Exponential Enrichment), they are usually a sequentialcombing process (thus the term “biopanning”) and lack a key component ofDarwinian evolution—the generation of variants. Even if point mutationis introduced in each round through error prone PCR or growth in mutatorbacteria, the evolutionary potential is limited (Tuerk C, Gold L.Systematic evolution of ligands by exponential enrichment: RNA ligandsto bacteriophage T4 DNA polymerase. Science. 1990; 249:505-510; Scott JK, Smith G P. Searching for peptide ligands with an epitope library.Science. 1990; 249:386-390; Gram H, et al. In vitro selection andaffinity maturation of antibodies from a naive combinatorialimmunoglobulin library. Proc Natl Acad Sci USA. 1992; 89:3576-3580;Irving R A, et al. Affinity maturation of recombinant antibodies usingE. coli mutator cells. Immunotechnology. 1996; 2:127-143). Rapidevolution in natural systems occurs when large units of information canre-assort and recombine, as is the case during meiosis.

Cell affinity agents are needed in many areas of cancer research andclinical study. Monoclonal antibodies are the workhorse of celllabeling, but are mostly useful when a given cell surface molecule isknow. For cancer cell detection in blood or tissue or for cancer cellcapture, single monoclonal antibodies are rarely sufficient todistinguish cancer cells from neighboring tissue or other normal cells.Clinically, this can be a problem for evaluating surgical resectionmargins and for pathological analysis of small samples (Blair S L, etal. Enhanced touch preps improve the ease of interpretation ofintraoperative breast cancer margins. Am Surg. 2007; 73:973-976;Cortes-Mateos M J, et al. Automated microscopy to evaluate surgicalspecimens via touch prep in breast cancer. Ann Surg Oncol. 2009;16:709-720). There as been considerable interest of late in circulatingtumors cells, but these are present in very low numbers and requirehighly processive and efficient capture methods to be obtainable insufficient numbers for down stream analyses. In vivo imaging with cancertargeted contrast agents would be of obvious utility, and there isconsiderable interested and development of tumor targeted nanoparticlesfor drug delivery (Nie S, et al. Nanotechnology applications in cancer.Annu Rev Biomed Eng. 2007; 9:257-288). In vivo applications requirebiocompatible materials, and DNA is obviously one such polymer.

Accordingly, a DNA nanoparticle library technology has been developedthat uses rolling circle amplification (RCA) of circular oligonucleotidetemplates to produce libraries of single stranded DNA nanoparticles thatcan be selected for cell binding properties. By including randomnucleotide sequences in the template oligonucleotide, libraries can beproduced and desired functions selected. In some embodiments multimodalDNA nanoparticles can be created that specifically bind to cancer cells.In more embodiments, methods to optimize the creation of multimodal DNAnanoparticles are described. The desired particles are “bred” by a noveliterative selection and re-assortment method to create modular DNAnanoparticles that contain multiple distinct recognition elements (FIG.1B).

A challenge in many areas of cancer research and treatment is theproduction of cancer cell specific binding agents. In a few cases trulycancer cell specific antigens can be targeted by antibodies or otheraffinity ligands, but more often cancer cells distinguish themselves byaltered levels of multiple surface molecules. The multimodal particlesproposed here are capable of multiple interactions with the target cellof interest and can potentially overcome the limitation of single targetagents such as antibodies, peptides, and aptamers.

Some embodiments include methods to validate and optimize combinatorialselection for multi-module particles. Data demonstrates the selection ofcell binding particles from a library where each DNA nanoparticlecontains a single recognition sequence module. Using a leukemia (K-562)and a non small cell lung cancer line (NCI-H23) as model systems, theoptimal combinatorial strategy are identified.

Some embodiments include methods to create particles that bind to lungcancer and leukemia cell lines. Several different cells lines derivedfrom each of the two tumor types are used to select particles with broadspecificity to that tumor type. Cell lines from non-neoplastic originsare used in subtractive screening strategies if non-specific binders arerecovered.

Some embodiments include methods to demonstrate cancer specific cellbinding of selected particles. Fluorescently labeled particles are usedon tissue arrays for fluorescent microscopy and on suspension cells forflow cytometry. Particles tagged with biotin or iron oxide are used formagnetic cell separation.

While this technology is similar to aptamer technology in that it usesnucleic acid libraries as the basis for molecular recognition, itdiffers in several important ways. Each particle contains many copies ofthe sequence elements so there is intrinsic multivalent display of themodules, allowing avidity to compensate for low monovalent affinity. Themodular nature of the particle template construction allows multipledistinct recognition elements to be assembled into a single molecularentity. Furthermore, the combinatorial selection method allows theoptimal particle with multiple recognition elements to be evolved in thesame molecular context in which it will be used, rather than graftingthem on to some other framework or particle for application. Thecombinatorial method also adds an element of true molecular evolution inwhich novel combinations of modules can be created by re-assortment,akin to recombination in meiosis.

It should be noted that there are many potential clinical applicationsof these nanoparticles since DNA can have several functions in additionto the formation of specific ligands. DNA can be immunogenic if itcontains unmethylated CpG motifs, it can act as a scaffold forhybridizing other oligonucleotide conjugates, it can have enzymaticactivity, it is easily chemically modified to allow small molecule ormetal ion attachment and metals can be directly deposited onto DNA, itcan carry DNA binding drugs, and it can carry genetic information(Klinman D M. Adjuvant activity of CpG oligodeoxynucleotides. Int RevImmunol. 2006; 25:135-154; Breaker R R, Joyce G F. A DNA enzyme thatcleaves RNA. Chem Biol. 1994; 1:223-229; Bern L, et al. DNA-TemplatedPhotoinduced Silver Deposition J. Am. Chem. Soc. 2005; 127:11216-11217;Richter J, et al. Construction of highly conductive nanowires on a DNAtemplate. Applied Physics Letters. 2001; 78:536; Lund J, et al. DNANetworks as Templates for Bottom-Up Assembly of Metal Nanowires. 5thIEEE Conference on Nanotechnology. Nagoya, Japan; 2005:836-840; ZanchetD, et al. Electrophoretic Isolation of Discrete Au Nanocrystal/DNAConjugates. Nano Letters. 2001; 1:32-35). Thus the particles selectedusing methods provided herein can serve as the basis for multifunctionalnanoparticles for imaging, drug delivery, or immunotherapy. DNA has along clinical history and a favorable toxicity and biodegradabilityprofile (Fichou Y, Ferec C. The potential of oligonucleotides fortherapeutic applications. Trends Biotechnol. 2006; 24:563-570).

Methods and compositions provided here are potentially transformative inthe area of cancer cell study and detection because they couple thepower of random libraries and biopanning selections with molecularbreeding concepts to create multifunctional molecules for cell binding.In addition to the conceptual advantages of this approach, discussedherein, once a particle has been selected and sequenced, otherlaboratories can easily create that particle from bacteria containingthe cloned sequence or a synthetic oligonucleotide and a few simplemolecular biology steps. The RCA reaction is scale-able and far lesscomplicated than hybridoma technology. The pioneering approach ofcreating a single molecule nanoparticle with modular functionality isgroundbreaking in its flexibility and potential for development as aplatform for applications beyond just those discussed in detail here.Some embodiments provided herein are unique and innovative in at leastthree major ways. First, the module designs are unlike any other libraryformat in flexibility and ease of implementation. Second, selectionformats are the same as the application format meaning the selectedparticles can be used immediately without the need to chemically alteror conjugate them to another molecule or particle. Finally, compared toother nanoparticle materials, DNA is non-toxic and antisenseoligonucleotides, aptamers, gene therapy, and CpG oligonucleotides haveall been used in human trials.

Production and Characterization of DNA Nanoparticles by RCA

DNA nanoparticles are produced by enzymatic DNA synthesis using a stranddisplacing DNA polymerase, phi29, and a circular oligonucleotidetemplate. The oligonucleotide circle is typically produced by ligationof a 100-200 base pair linear oligonucleotide with a short (30 bp)oligonucleotide complementary to the ends. The ligation oligonucleotidealso serves as the initiating primer for the RCA reaction. Phi29polymerase is highly processive (˜70 kb) and produces a linear increasein single stranded DNA for over an hour in a typical reaction.

The resulting RCA products are concatemers complementary to the templatecircular oligonucleotide. These long single stranded products collapseinto randomly coiled nanoparticles, a property that has been exploitedfor counting individual RCA events (Jarvius J, et al. Digitalquantification using amplified single-molecule detection. Nat Methods.2006; 3:725-727). The size of the particles is a function of the timeand efficiency of the RCA reaction. The reaction can be stopped by theaddition of EDTA or heat inactivation of the phi29 polymerase, thoughthe latter may lead to aggregation of the DNA particles. The particlescan be visualized with either single stranded or double strandedfluorescent DNA binding dyes due to the double stranded character thatresults from internal base pairing. For analytical purposes theparticles can be made fluorescent by the inclusion of fluorescentlylabeled nucleotides during the synthesis. Alternately a fluorescentlylabeled oligonucleotide probe can by hybridized to the particles (FIG.2, panels A -D).

It is difficult to size the particles by conventional or denaturing gelelectrophoresis due to their large size and single stranded character.Dynamic Light Scattering (DLS) is a common technique for measuring theproperties of nanoparticles such as size and zeta potential. DLS usesthe time autocorrelation of a signal of scattered light to determine thepolydispersity and average diffusion coefficient, which through theStokes-Einstein equation is related to the average dynamic radius. RCAreactions were carried out for four time points (10, 30, 45, 60 minutes)and were stopped by the heat inactivation of the polymerase at 65° C.for 10 minutes. The samples are then immediately measured by DLS. For amonodisperse sample the autocorrelation plots should show a singleexponential decay, the exponent coefficient of which is known as thefirst moment and is used to calculate a Z-average size. The secondmoment is used to calculate the deviation from monodisperse and is knownas the polydispersity index (PdI), which is a measure of relative peakwidth of the Gaussian size distribution. In general if the PdI isgreater than 0.25 it is recommended to use a secondary algorithm calledNon-Negative Least Squares (NNLS) which models the autocorrelation curveas a contribution of several size samples and extracts individual peakdata (FIG. 3, panels A-3B).

Single Component DNA Nanoparticle Library Construction and Testing

A method to generate high diversity libraries of DNA nanoparticles andselect for those with desired features through an iterative screeningand re-amplification method is summarized in FIG. 4.

The library is generated from a template oligonucleotide that has arandom stretch of bases in the middle, flanked by PCR primer sites.These ends also bind to the ligation oligonucleotide to circularize thetemplate for RCA amplification. The random sequence is 60 nucleotideslong and is flanked by defined sequences that can be used to hybridizefluorescent or otherwise labeled probes for visualization orpurification. Using this design ˜10 billion unique DNA nanoparticles canbe produced in a small volume (e.g., 50 μl) RCA reaction. The particlesare screened for the desired binding activity and the binders amplifiedby PCR using the Stoffel fragment of Taq polymerase that lacks 5′ to 3′exonuclease activity. The use of Stoffel fragment greatly increased theamplification efficiency, presumably due to the concatemeric nature ofthe DNA nanoparticles. Following amplification several rounds ofasymmetric PCR are performed to increase the copy number of the templatestrand that is then circularized by ligation and subjected to RCA toregenerate the DNA particles. The cycle of screening, amplification, andparticle regeneration is repeated for several (e.g., 5-10) rounds.

The scheme described herein has been used to select DNA nanoparticlesthat bind to human dendritic cells (DCs). DCs were generated fromperipheral blood monocytes. After 5-7 days of culture, DC were incubatedfor 1 hour with the DNA nanoparticle library, and washed several timeswith cold PBS. After 7 cycles of selection and re-amplificationaggregation of the DCs during the washing steps was observed, suggestingthat binding particles had been enriched for that were causingagglutination. Flow cytometry analysis indicated that the population ofparticles contained in the 7^(th) round pool was enriched for particlesthat bound to DCs (FIG. 5).

Individual particles were obtained by cloning the PCR amplificationproducts from the 7^(th) round of selection. 15 clones were sequencesand all but one were unique. Each clone was used to generatefluorescently tagged DNA nanoparticles and these were tested for DCbinding by flow cytometry. Several of the clones showed good binding tothe DCs (FIG. 6).

Further characterization of these DC binding particles is underway, butthe data to date demonstrates the feasibility of the DNA nanoparticlelibrary selection strategy. In addition, non-specific uptake or immuneactivation of non-targeted particles has not been observed, suggestingthat selection of particles with binding affinity for the target celltype is essential and that non-specific cell binding is minimal.

The DNA nanoparticles are stable over the time of the experiments.However, the particles are fairly resistant to exonuclease andendonuclease degradation. Since the particles are formed from acontinuous single stranded DNA molecule, each particle has only one 3′and one 5′ end which may account for their resistance to exonucleasedigestion. Most endonucleases, including DNase, prefer double strandedDNA as a substrate. The nuclease resistance could increase bypolymerizing nucleotides with altered backbone chemistries. The phi29polymerase can incorporate phosphorothioate backbone nucleotides,although the rate of polymerization is marginally slower.

Research Design and Methods

Some embodiments provided herein include methods and compositions todevelop multimodal particles that bind to a target cell type throughcombinatorial “breeding” of DNA nanoparticles. The overall strategy isto first optimize the selection methodology, then apply the method to apanel of cell lines from each of two cancer types and confirm theirusefulness in several cell binding applications. The rationale for usingmultiple cell lines from a couple of cancer types is to allow theselection of particles that are tumor specific but not cell linespecific and to then be able to cross compare. If necessary, subtractivescreening methodologies are employed to prevent the recovery ofnon-specific cell binding particles. Cell lines or normal lines (e.g.NIH-3T3) are used for subtraction.

Methods to Validate and Optimize Combinatorial Selection

Two cell lines, K-562 and NCI-H23, are used to test and optimize themultimodal DNA nanoparticle selection methods. Each round of selectionconsists of 4 essential steps and the molecular biology is the sameregardless of selection scheme (FIG. 7).

Library Ligation

The template oligonucleotide is mixed with the ligation primer in T4ligase buffer to final concentrations of 100 nM and 300 nM respectively.The mixture is heated to 95° C. and allowed to cool slowly to roomtemperature. T4 ligase is added and the reaction incubated for 1 hour at37° C. For multimodal libraries, there are multiple ligation primers,and all but one primer are dideoxy terminated so that each multimodaltemplate circle is primed at only one location.

RCA

The ligation mixture is added to an RCA reaction mix containing phi29polymerase. The final concentration of the ligated templateoligonucleotides is 1 nM, meaning that in a 100 μl reaction ˜6×10¹⁰ DNAnanoparticles are created. When the initial library is made each ofthese particles will contain a unique sequence. The reaction proceedsfor 30 minutes at 30° C. and is terminated with EDTA. This producesparticles ˜250 nm in size. The RCA reactions are monitored in real timewith Oligreen, a single and double stranded DNA binding fluorescent dye,to confirm linear amplification. Since the amount of template DNAligated and amplified is the same round to round, this rate should beconstant and thus serves as a quality control checkpoint (FIG. 8).

Selection

Step A. The selection step can be performed in several ways, dependingon the application. In one embodiment, the particles are incubated withthe cell target of choice. If non-specific cell binding is recovered,subtractive approaches can be used in which the library is first orconcurrently counter selected against an irrelevant cell target toremove non-specific cell binding. This can be done by preincubating thelibrary with the irrelevant cell to absorb non-specific binding or, ifthe target and irrelevant cells can be easily separated, the library canbe added to a mixture of both with the target cells then later removed.Typical incubation times are 30 minutes to an hour at either roomtemperature or 37° C. 10⁵ cells are mixed with the entire RCA reactionfrom step 2. Step B. Washing is performed by centrifuging the cells andaspirating the liquid, then resuspending the cells and transferring to anew tube for the next wash. Three to five wash steps will be performed.Transferring to new tubes at each steps minimizes the recovery ofplastic binding particles. Step C. Particle recovery. Since eachparticle is a concatemer of several hundred copies of the basic unitsequence, PCR amplification of single particles or even particlefragments is possible. Therefore, the particles can be recovered bylysing the washed cells followed by 1 hour treatment with proteinase K.The cell lysate is added to the PCR reaction in the next step, ensuringrecovery of both external bound particles as well as particles that mayhave been internalized by the cells.

Amplification

One aim of the amplification step is to regenerate the population oftemplate oligonucleotides that can be ligated and used to generate apool of particles reflective of the particles recovered in the selectionstep. The main amplification is by PCR and the desired template DNAstrand is secondarily enriched over the complement by asymmetric PCRusing only the primer for the desired strand. a) Stoffel PCR. PCRamplification of these DNA nanoparticles is much more efficient when theStoffel fragment of Taq polymerase, which lacks 5′-3′ exonucleaseactivity, is used instead of conventional Taq polymerases, which has5′-3′ exonuclease activity. This may be because of the concatamericnature of the DNA particle strand, which could bind many primers in theinitial rounds of PCR. The extending polymerase would run into theprimed strand downstream of it and begin digesting, leading to veryinefficient polymerization from the particle strand. The PCR reactionsare monitored in real time with Sybr green and stopped once theproduction of PCR product plateaus. The real time plots also allowquantitative estimates of the relative amount of DNA, and by inferencethe number of particles, recovered in each round. b) asymmetric PCR. ThePCR product is diluted into a new reaction mixture that contains onlythe primer that will produce the ligatable template strand. This primerhas a 5′ phosphate. The reaction is run for 10 cycles (FIG. 9).

After a successful selection, candidate particles are further analyzedfrom the final pool. To obtain individual particles, the final pool areamplified by Stoffel PCR and cloned into a plasmid sequencing vector.Once cloned, 10-20 candidates are sequenced to determine the extent ofsequence diversity in the final pool. Each candidate can be regeneratedby PCR/asymmetric PCR amplification from the plasmid.

Library Design and Selection Considerations

The design of each random module can be subject to some constraints. Theminimum length of an oligo that can effectively circularize is reportedto be around 80 bp. Since the flanking PCR/ligation primers sites are30-40 bp, the randomized region can be at least about 40 bp. Thepotential diversity of any such library is much greater than the samplesize. For example, a 60 bp library has 4⁶⁰ different possible sequences,˜1×10³⁶. Since typically 10¹⁰-10¹¹ particles can be created in areasonable volume, only a tiny fraction is sampled of the possiblenumber, and any particular batch of the library is a unique subset ofthe possible with each individual sequence represented by a singlemolecule. However, 10¹⁰ particles will likely contain any given 19 bpmotif at least once and smaller motifs will be well represented withinthe sampled population.

When multimodal particles are created there is an additionalcombinatorial element. If 3 libraries of the size above are randomlycombined into multimodal particles, then there would be 10³⁰ differentcombinations, treating each module as a discrete entity. Since there maybe limits to 10¹⁰ particles due to the physical constraints of particlesynthesis, it may not be ideal to combine libraries in the first fewrounds of selection. In fact, it is unlikely that any particularcombination recovered in the first round would reform in the secondwhile the remaining diversity is still high. On the other hand, ifparticular combinations of modules would be optimal together but are notparticularly good on their own, then delaying combination of the librarymay result in the desirable modules disappearing from the populationbefore they have a chance to team with the others for selectiveadvantage. However, in the absence of a rigorous model of selectionkinetics and fitness landscapes, an empirical approach can be used.

The overall concept of the modular library screening method can bedivided into a “panning” phase, where binders within the population areselectively enriched, and a “breeding” phase in which the multimodalparticles are re-assorted in each cycle so that novel combinations canbe generated and the optimal combinations enriched (FIG. 10).

Three selection schemes can be tried. In the first, the libraries areassembled into the multimodal format prior to the first round and in allsubsequent rounds. However, for the first three rounds the particles areamplified as a single unit and the modules are not be re-assorted (FIG.11).

Non-modular PCR ensures that any particular combination of modules thatcomes through the first round will be amplified to higher copy numberbefore the re-assortment process begins. For subsequent rounds, therecovered particles are split and some amplified as a single unit by thenon-modular method and the rest amplified as modules and recombined,ensuring representation of the selected combinations as well asgenerating new combinations of modules.

The second selection scheme attempts to pre-enrich the modular pool fordesired activity by screening the single component libraries for severalrounds prior to combination in multimodal format. The individuallibraries are screened for 5-10 rounds until there is evidence in eachof enrichment for binding clones (indicated by an increased in thenumber of particles recovered in each round as determine quantificationfrom the real time PCR amplification step). The combinatorial strategyis then be pursued for several rounds. The final strategy is a hybrid ofthe first two. Three to five rounds of selection are performed with eachof the component libraries, and then the following rounds are done usingonly the combinatorial approach.

Protocols can be optimized against K-562 and NIH—H23 cell lines. Singlemodule library selections can be run in parallel. To determine theoptimal method, the particles can be evaluated for cell binding affinityand specificity. The affinity can be measured by adding equal numbers ofparticles to the cells and quantitating the bound number by quantitativePCR after stringent washing. Specificity can be assessed by performingthe same experiment against the reciprocal cell line and taking theratio of the two. If specificity is not achieved, then the selectionscan be repeated with a subtractive step using the other line included.Finally, the individual modules of any multimodule particles can beindependently amplified, ligated, and tested in the single moduleparticle format to determine if each module is contributing to theoverall binding of the multimodule particle.

While the library selection schemes do not require a priori knowledge ofthe particular molecules on the target cells surface, particles that arespecific for the cell target of interest can be used to identify thecell surface molecules. The particles can be used in pull downexperiments with target cell extracts and the bound proteins identifiedby mass spectrometry (Mallikaratchy P, et al. Aptamer directly evolvedfrom live cells recognizes membrane bound immunoglobin heavy mu chain inBurkitt's lymphoma cells. Mol Cell Proteomics. 2007; 6:2230-2238).

Methods to Create Particles that Bind to Lung Cancer and LeukemiaDerived Cell Lines.

The optimal selection strategy described herein can be applied to fouradditional lung cancer cell lines such as NIH-226, NCI-H322M, NCI-H460,and NCI522, and four additional leukemia derived lines, such as,CCRF-CEM, HL-60, Molt-4, and RPMI-8226L. These cell lines are members ofthe NCI-60 panel of well defined cancer cell lines. Since a desirableparticle for many applications can be one that binds broadly to tumorsof a particular type, these panels can be used in two ways. First,selections against each with subtraction against a normal line or one ofthe other tumor lines can be performed (FIG. 12).

Candidate particles from each of those can be tested against the othercell lines of the same cancer type to identify cases where broadselectivity may have been achieved by serendipity. Conversely, broadspecificity can be selected for in the selection protocol by poolingcell lines and/or alternating the target cell line or target cell poolsin each round, thus providing a selective advantage to particles thatbind to all of the cell lines used. This approach is applicable to lungcancer lines.

The leukemia derived lines come from several different types ofleukemia, including acute and chronic myeloid, acute lymphoid, andplasma cell myeloma. In addition to devising selections that will favorbroad specificity to all of the lines, particles that recognize thelymphoid derived but not the myeloid derived lines may be recovered (andvice versa).

Methods to Demonstrate Cancer Specific Cell Binding of SelectedParticles

Particles selected for using the methods described herein can beevaluated in at least three formats: flow cytometry, histology byfluorescent microscopy, and cell capture. These three techniques aregenerally reflective of most ex vivo applications of cell affinityreagents.

Flow Cytometry

DNA nanoparticles can be coupled to fluorophores in at least threeways. 1) Fluorescent nucleotides can be used during the synthesis step,2) DNA binding fluorescent dyes can be added after synthesis (thoughthese must be cell impermeant for the applications here), or 3)fluorescently labeled oligonucleotides can be hybridized to theparticles after synthesis. The first of these, labeled nucleotides, ishas been done successfully with Alexa488 labeled nucleotides (see dataherein).

Labeled DNA particles can be used in the same way as labeled antibodies.The particles are incubated with the fixed cells, the cells washed, andthe sample run on a flow cytometer (see data herein). The particles donot affect the forward or side scatter of the cells and unboundparticles, while detectable by their fluorescence, do not scattersufficiently on their own and can be gated out. Multiple particles canbe used if they labeled with compatible fluorophores.

Histology/Fluorescent Microscopy

The fluorescently labeled particles can be assessed in fluorescentmicroscopy. Initially, the particles can be tested against the cognatecell lines that have been cytospun onto slides. Specificity can beassessed by creating slides with mixtures of the cognate and other cellsat defined ratios. Standard cell staining protocols can be used and thevarious parameters (incubation times, DNA nanoparticle concentration,etc) optimized.

Commercial tissue arrays (MaxArray, Invitrogen) can be used to determinethe specificity of the particles that bind to lung cancer derived lines.Multi-tumor and normal arrays can be screened first to determine thespecificity, and then lung cancers arrays can be used to determine thesensitivity against many different samples. It is possible, if notlikely, that different particles can have different profiles when socompared. For histological applications it may be useful to use a poolof particles to ensure the broadest binding to a given cancer type

Cell Capture

The DNA nanoparticles can be used to capture and isolate their targetcells in several ways. The particles can be labeled with biotin byeither incorporation of biotinylated nucleotides during the synthesis orby hybridization of a biotinylated oligonucleotide after the synthesis,as for the fluorophores described herein. Biotinylated particles canoften be captured along with the cells they are stuck to usingstreptavidin coated magnetic beads. Alternately, the particlesthemselves can be made magnetic through the coupling of iron oxidenanoparticles. An iron oxide nanoparticle can be conjugated to theseeding primer in a 1:1 ratio such that when the reaction proceeds theiron oxide will be embedded inside the DNA nanoparticle. The 1:1conjugated oligo-iron oxide structures can be used as hybridizingoligonucleotides to a DNA nanoparticle scaffold (FIG. 13).

To assess capture efficiency, the target cell lines can be mixed withirrelevant cell line and the capture efficiency determine. The cells canbe incubated with the DNA nanoparticles then, in the case of thebiotinylated particles, mixed with magnetic streptavidin coated beads.

Some embodiments include methods to validate and optimize combinatorialselection of libraries. Some embodiments can demonstrate that 10 DNAnanoparticles each containing 3 unique recognition elements can beamplified and reassorted to create more than 50% increase in librarydiversity i.e. the sequences of more than 10 out of 20 resorted cloneswill be different from the original 10. Some embodiments can identify atleast 1 multimodal particle that binds to the target cell line 10-foldbetter than a random control particle. Binding can be defined byquantitation of recovered DNA by quantative PCR (QPCR) after incubationwith the target cells and washing as in the selection protocol.

Some embodiments include methods to select particles against a panelcancer cell lines. Some embodiments can utilize at least 6 of the 10cell lines, and select at least one binding particle. Some embodimentscan select at least 1 particle that has a 3 fold increased binding to atargeted cancer cell line relative to the normal cell line. Someembodiments can select at least 1 particle that exhibits 3-foldincreased binding to 3 or more cell lines from the same cancer relativeto the normal line

Some embodiments include methods to demonstrate cancer specific cellbinding of selected particles. Some embodiments include utilizingparticles that results in a mean fluorescent intensity 5 fold greaterwhen used against the target cell line compared to an irrelevant cellline. Some embodiments include demonstrating at least one particle orpool of particles that results in a fluorescent intensity at least 2fold greater on the targeted cell line vs a control cell line. Someembodiments include demonstrating at least one particle or pool ofparticles that fluorescently stains lung cancer tissue with a 2 foldgreater intensity than normal tissue. Some embodiments includedemonstrating capture of 1 cell in 100 using a leukemia specificparticle.

Immunotherapy and Targeting Cancer

Immune therapy of cancer seeks to activate the body's own immune systemto destroy both primary and disseminated tumors. This attractive ideahas not met with much success in the clinic in part because of the lackof good immune adjuvants. A novel selectable DNA nanoparticle librarytechnology has been developed. DNA nanoparticles (DNA-NP) are generatedby rolling circle replication (RCA) of a circular templateoligonucleotide. The resulting complementary single stranded concatemercollapses into a random coiled nanoparticle. Using this approach, DNA-NPhave been identified that, by virtue of their sequence, bindspecifically to DC, are taken up, and induce Ca²⁺ flux and IL-6secretion. DC binding DNA-NP can be further refined and tested for theirability to activate immune responses in a mouse melanoma model. DNA andother nucleic acids have a long clinical history and offer a streamlinedpath to the clinic.

Some embodiments include methods to develop a DNA-NP capable of inducingan immune response to an existing tumor. Without wishing to be bound toany one theory it is believed that targeted DNA nanoparticles that bindto and stimulate dendritic cells (DC) can cause immune activation andlead to anti-tumor immune responses.

Some embodiments include methods to screen and rank DNA-NP that activateDC. Data shows the selection of DNA-NP that selectively bind to andstimulate DCs. The hypothesis that DCs stimulated with DNA-NP matureinto antigen presenting cells capable of T cell stimulation in vitro canbe tested. One of the strengths of the methods described herein is thatmultiple distinct sequences can be easily combined to make combinatorialhybrid particles. Combinations of DC binding particles can likely causegreater DC activation than each given individually or in combination asdistinct particles. The most active particle can proceed to in vivotests.

Some embodiments include methods to relating to direct injection ofDNA-NP into tumors that can activate tumor infiltrating DC. The mouseB16-OVA melanoma model can be used. DNA-NP can be injected intoestablished tumors and the activity on tumor infiltrating lymphocytesdetermined by histology (CD11c & T) and cytokine analysis. If robustresponses are observed the particles can be optimized for size andbackbone composition and the effect on tumor growth determined.

Some embodiments include methods that relate to immunization with DNA-NPand model tumor antigens elicit antigen specific responses and tumorrejection. The mouse B16-OVA melanoma model can be used. The hypothesisthat immunization with ovalbumin or peptides derived from it togetherwith the DNA-NP produces an antigen specific immune response in normalhealthy mice can be tested. If robust responses are observed immunizedtumor bearing mice can be tested. If systemic immune responses are weak,the hypothesis that intra-tumoral immunization will produce anti-tumorresponses can be tested. The dependence of those responses on T cellswill be analyzed in mice depleted of CD4⁺ or CD8⁺ cells.

Methods and compositions provided herein can provide pre-clinical dataimportant to begin planning human clinical trials. Possible toxicity ofthe DNA nanoparticles can be carefully monitored, particularly excessiveinflammatory or autoimmune responses and, where possible,pharmacodynamics can be evaluated.

Background and Significance

Immune therapy in cancer has a long history marked by striking anecdotalsuccesses but few generally successful strategies. Anton Chekhov andWilliam Coley noted the relationship between infection and cancerregression in the late 1800s, with the latter developing “Coley'sToxin”, a mixture of killed Streptococcus pyogenes and Serratiamercescens as a treatment for cancer (Gresser I (1987) A. Chekhov, M.D., and Coley's toxins. N Engl J Med 317: 457). Modern approaches seekto activate the immune system using defined stimulators of immune cellssuch as cytokines or toll-like receptor (TLR) agonists, in place ofbacterial preparations (though Bacillus Calmette-Guerin (BCG) is stillused in the clinical treatment of bladder cancer) (Herr H W, Morales A(2008) History of bacillus Calmette-Guerin and bladder cancer: animmunotherapy success story. J Urol 179: 53-6).

Immunotherapies have shown promising results in several cancers (FigdorC G, et al., (2004) Dendritic cell immunotherapy: mapping the way. NatMed 10: 475-80). Cytotoxic T lymphocytes (CTLs) play a major role ineliminating malignant cells by specifically recognizing antigenicpeptides presented on MHC class I molecules by dendritic cells (DC)(Nguyen T, et al., (1999) Recognition of breast cancer-associatedpeptides by tumor-reactive, HLA-class I restricted allogeneic cytotoxicT lymphocytes. Int J Cancer 81: 607-15). Peptides derived fromtumor-associated antigens (TAA) have been identified for some forms ofhuman cancers (Minev B R, et al., (2000) Synthetic insertion signalsequences enhance MHC class I presentation of a peptide from themelanoma antigen MART-1. Eur. J. Immunol. 30: 2115-2124). Thus far,however, effective peptide vaccination of cancer patients has beenlimited to very few trials and for most cancers the antigens are notidentified. DCs are the most potent antigen presenting cells. Inaddition to taking up the antigen, DCs also need to receive a maturationsignal in order to activate CTLs to perform their cytotoxic functions.If DCs take up antigen without receiving a stimulus, they can inducetolerance. Two central hurdles in immunotherapy are: (1) In manyinstances tumor-specific CTLs though present in patients, are in atolerant/nonresponsive state. One of the major challenges for tumorimmunotherapeutic approaches is to break this tolerance to achieveCTL-mediated killing of tumor cells. (2) For most tumors the antigensare unknown and possibly patient and tumor specific. Consequently,methods to overcome these obstacles should lead to a marked improvementin antigen presentation and induction of potent anti-tumor CTL.

Certain immunostimulatory molecules, from TLR agonists such as CpG DNAand poly(I:C), to cytokines, have been tried in one form or another, butgeneral principles have been difficult to elucidate and the need formore potent immune adjuvants remains acute. Interferon alpha andinterleukin 2 are approved for the treatment of melanoma. Systemicadministration of CpG oligonucleodies has been moderately successful inmouse models and clinical trials, suggesting that specific tumorantigens need not be included in a successful therapy.

The immune system may be far more sensitive to stimulation withmultivalent and multifunctional particle delivery mechanisms, perhapsmimicking virus and bacteria. The primary cell responsible forinitiating and directing an anti-tumor cytotoxic T cell response is thedendritic cell, though B cells can also serve in that role to someextent. Dendritic cells uptake antigen by endocytosis and pinocytosis,but they must also encounter an immune stimulus to mature into robustantigen presenting cells. Therefore, targeting adjuvant activity to DCsis an obvious route to enhance the potency of an adjuvant. This has beenattempted in several ways, including antibodies that bind to DCrestricted membrane antigens such as DEC-205. Targeting antigen to DCsin lymphoid tissue using antibodies against DEC-205 in conjunction withan adjuvant led to increased induction of immune responses. Thus usingmolecules that target DC is a very promising approach to enhance immuneresponse to cancer. However, antibodies, need to be humanized and areexpensive to produce.

Chemically diverse libraries are a rich source of potential ligands forbiomolecules and cellular targets of interest. When modular biopolymerssuch as nucleic acids or polypeptides are used, the combinatorialdiversity of these libraries can become astronomical and well beyond thecapabilities of systematic high throughput screening methods. Combingthese libraries requires iterative schemes that couple a selection stepwith an amplification step. For peptides, display of a given peptide ona bacteriophage, virus, or bacteria allows amplification by growth ofthe host organism. Nucleic acids are typically amplified by somevariation of PCR (Tuerk C, Gold L (1990) Systematic evolution of ligandsby exponential enrichment: RNA ligands to bacteriophage T4 DNApolymerase. Science 249: 505-10). Subtractive and in vivo selectionschemes have been developed for aptamer and phage displayed peptidelibraries that can enhance the cell specificity of recovered targetingligands (Siegel D L, et al., (1997) Isolation of cell surface-specifichuman monoclonal antibodies using phage display andmagnetically-activated cell sorting: applications in immunohematology. JImmunol Methods 206: 73-85). Cellular targeting has been demonstrated bylibraries of peptides and oligonucleotide aptamers (Rasmussen U B, etal., (2002) Tumor cell-targeting by phage-displayed peptides. CancerGene Ther 9: 606-12; Hicke B J, et al., (2001) Tenascin-C aptamers aregenerated using tumor cells and purified protein. J Biol Chem 276:48644-54).

However, peptide and aptamer libraries have some distinct limitations.Many peptide display formats, such as phage, present many copies of eachpeptide per particle. This can allow the recovery of relatively lowaffinity interactions that benefit from the high avidity of thepresentation format. However, it may be difficult to maintain thedesired binding avidity and specificity when the selected peptides aremoved to another particle or molecule. Aptamer libraries can suffer fromthe reverse complication since they are usually presented in amonovalent format. Aptamers have been most clinically useful when a highaffinity interaction can function in an antagonist manner, though theyhave been used as targeting moieties attached to nanoparticle drugdelivery vehicles. However, when aptamers that were selected in amonovalent format are attached to particles in a multivalent way,specificity can be lost as low affinity interactions gain avidity. Inaddition, there is always a concern that the transfer or attachment of apeptide or aptamer to a new molecule or particle may alter itsconformation and binding affinity for the target of interest. Thus fortargeting moieties on particles, it would be advantageous to select theoptimal ligand in the context in which it will be used.

The paradigm of nanotechnology for applications in the medical field hasbeen oriented around the framework of bottom-up construction. Generally,a scaffold of polymer or metal serves as a basis for the addition offunctional moieties to lend the nanomaterial the desired capabilitiessuch as selective targeting, transport of therapeutic and imagingagents, and immune evasion. When biopolymers such as DNA are used, theyare often rationally designed to form a predetermined structure (ZhangC, et al., (2008) Conformational flexibility facilitates self-assemblyof complex DNA nanostructures. Proc Natl Acad Sci USA 105: 10665-9).However, this approach has overlooked a powerful tool of molecularbiology: the simple creation and efficient combing of libraries withdiversity of 10⁹ or more. Small nucleic acid aptamer sequences have beenidentified with binding and enzymatic properties, but their use innanoparticle based applications has mostly involved grafting them ontoother materials. An overview of methods of diverse library selectionwith nanoparticles to create libraries of DNA nanoparticles by rollingcircle replication of randomized circular templates and selecting forparticles that bind to a target cell type is shown in FIG. 14.

Production, Characterization, and Purification of DNA Nanoparticles byRolling Circle Amplification

DNA nanoparticles are produced by enzymatic DNA synthesis using a stranddisplacing DNA polymerase, phi29, and a circular oligonucleotidetemplate.

The oligonucleotide circle is typically produced by ligation of a100-200 base pair linear oligonucleotide with a short (30 bp)oligonucleotide complementary to the ends. The ligation oligonucleotidealso serves as the initiating primer for the RCA reaction. Phi29polymerase is highly processive (˜70 kb) and produces a linear increasein single stranded DNA for over an hour in a typical reaction. Phi29 canalso incorporate phosphorothioate backbone nucleotides, although therate of polymerization is slower (FIG. 15).

The resulting RCA produces are concatemers complementary to the templatecircular oligonucleotide. These long single stranded products collapseinto randomly coiled nanoparticles, a property that has been exploitedfor counting individual RCA events (Jarvius J, et al., (2006) Digitalquantification using amplified single-molecule detection. Nat Methods 3:725-7). The size of the particles is a function of the time andefficiency of the RCA reaction. The reaction can be stopped by theaddition of EDTA or heat inactivation of the phi29 polymerase, thoughthe latter may lead to aggregation of the DNA particles. The particlescan be visualized with either single stranded or double strandedfluorescent DNA binding dyes due to the double stranded character thatresults from internal base pairing. For analytical purposes theparticles can be made fluorescent by the inclusion of fluorescentlylabeled nucleotides during the synthesis. Alternately a fluorescentlylabeled oligonucleotide probe can by hybridized to the particles (FIG.16, panels A-C).

It is difficult to size the particles by conventional or denaturing gelelectrophoresis due to their large size and single stranded character.Dynamic Light Scattering (DLS) is a common technique for measuring theproperties of nanoparticles such as size and zeta potential. DLS usesthe time autocorrelation of a signal of scattered light to determine thepolydispersity and average diffusion coefficient, which through theStokes-Einstein equation is related to the average dynamic radius. RCAreactions were carried out for four time points (10, 30, 45, 60 minutes)and were stopped by the heat inactivation of the polymerase at 65° C.for 10 minutes. The samples are then immediately measured by DLS. For amonodispersed sample the autocorrelation plots should show a singleexponential decay, the exponent coefficient of which is known as thefirst moment and is used to calculate a Z-average size. The secondmoment is used to calculate the deviation from monodisperse and is knownas the polydispersity index (PdI), which is a measure of relative peakwidth of the Gaussian size distribution.

As seen with flow cytometry, the average particle size increases as thereactions are allowed to proceed for longer. We have noticed in otherbatches that the size seems to peak around 300 nm, even with longerreaction times. These measurements are in good agreement with a freelyjoined chain model of polymer condensation which estimates a 60 kb ssDNAstrand to have a hydrodynamic radius of 379 nm. It is suspected that thesize of the particles may be limited by the processivity of the phi29enzyme and steric hindrance as the particle grows. However, oncereaction conditions are fixed, the size of the particles is reproduciblebatch to batch and can be tuned from roughly 100-300 nm. The optimalsize for a given application must be determined experimentally, and thenotion of “size” may be somewhat of an anachronism for a flexiblepolymer condensate. Electron microscopy is underway to obtain a higherresolution image of the particles at various stages of growth (FIG. 17,panels A-B).

DNA-NP are purified by size exclusion chromatography and dialysis, andconcentrated by centrifugal membrane concentration. After the RCAreaction there are significant excess free nucleotides that should beremoved before the particles are used for other experiments. Specialcare is taken to avoid any possible LPS contamination, including the useof dedicated glassware and columns Negative control particles are alwayspurified in the same way on the same apparatus with the same buffers.

DNA Nanoparticle Library Selection Method

A method to generate high diversity libraries of DNA nanoparticles andselect for those with desired features through an iterative screeningand re-amplification method has been developed. See Examples.

Individual particles were obtained by cloning the PCR amplificationproducts from the 7^(th) round of selection. 15 clones were sequencesand all but one were unique. Each clone was used to generatefluorescently tagged DNA nanoparticles and these were screened againstDCs by flow cytometry. Several of the clones showed good binding to theDCs. Clone 3 was chosen for further evaluation. Particles that bind tobreast cancer, ovarian cancer, and pancreatic cancer derived cell linesas well as particles that bind to adenovirus have been selected.

Specificity DC Binding DNA-NP

Further characterization DC binding clone 3 was undertaken. The specificof the cell binding was investigated with several other cell type andcell lines. DNA-NP were made fluorescent by the incorporation ofalexa488 tagged nucleotides during the synthesis. Controls include aparticle with the reverse complement sequence to clone 3 and thereaction mix with the labeled nucleotides. In addition to the cell typesshown in the figure, we have seen no binding to primary ChronicLymphocytic Leukemia cells or the RAMOS cell line. We have observedbinding of clone 3 to human monocytes and macrophages, albeit it at alower level for the former. Significantly, the clone 3 DNA-NP binds tomouse as well as human DC (FIG. 18).

The results above were confirmed by fluorescent microscopy (FIG. 19,panels A-B). Since all selections and binding experiments to this pointwere performed on ice, it was confirmed that the clone3 DNA-NP bound DCat 37° C. by flow cytometry (data not shown). Furthermore, when DC wereincubated with clone 3 DNA-NP at 37° C., the pattern of stainingsuggested that the DNA-NP had been taken up. Preliminary confocalmicroscopy has supported this interpretation but has not beenconfirmatory to date.

It was confirmed that clone 3 reproducibly binds by using separatebatches of particles and synthesizing particles from both the originalclone (PCR from bacteria colonies harboring the clone, followed byassymetric PCR with a 5′ phosphate on only the desired primer forsubsequent strand ligation and RCA) or from a synthetic oligonucleotidetemplate with the same sequence. In addition, it was tested that thestability of particles kept at −20° C. and 4° C. for several weeks; noloss of activity has been observed.

DC Binding DNA-NP Activate DC

DC binding DNA-NP may cause DC activation through changes in cytokinesecretion, signaling, and surface marker expression. IL-6 secretion is acommonly used indicator that DC have matured into immune activatingcells, though a full cytokine secretion profile is ultimately desirableto confirm this point. It has been shown that DC incubated with theclone 3 DC binding DNA-NP secrete IL-6 (representative experiment shownin FIG. 20, panels A-B). In addition, it has been measured Ca²⁺ flux 20seconds after DC are exposed to clone 3, but not after exposure tocontrol DNA-NP.

In general, non-specific uptake or immune activation of non-targetedparticles was not observed, suggesting that selection of particles withbinding affinity for the target cell type is essential and thatnon-specific cell binding is minimal.

Hybrid Particle Formation

A powerful feature of the DNA-NP methods includes the template sequencefrom which the particles are generated can be easily manipulated. One ormore synthetic oligonucleotides can be used to build the template andbeyond a minimum size of 60-80 bases, the RCA reaction proceeds equallywell on templates regardless of size. Therefore, once discrete particlesequences are identified it is quite straightforward to prepare a hybridtemplate by coupling the templates at the ligation step (FIG. 21).

One concern was that hybrid DNA nanoparticle may lose the properties ofthe individual components. To test this, the clone 3 sequence wasligated step-wise into a continuous circle with an equal length randomsequence. The progress of these step-wise reactions was verified by geland the final products were observed to undergo RCA as previouslyobserved with single sequence ligations. The hybrid nanoparticles stillbounding DCs and a hybrid control did not. This data supports thefeasibility of developing multifunctional DNA nanoparticles from eitherdefined sequences or during the selection.

Immunostimulatory Peptide Hp91

A short immunostimulatory peptide, Hp-91, was identified that causesactivation of human and mouse DCs. These peptides will be used if theDNA-NP do not have sufficient immune activating properties on their own,either in vitro or in vivo.

Hp-91 treated DCs induce antigen-specific T cells responses as measuredby IFN-γ secretion in an ELISPOT assay. Hp-91 treated human DCs inducedstrong melanoma antigen-specific CD8⁺ T cell responses, demonstratingthe immunostimulatory capacity of the peptide Hp-91 (FIG. 22). Similarresults were obtained in the mouse system, where BM-DCs pulsed withOVA-peptide and exposed to Hp-91, induced strong proliferation ofOVA-specific CD8⁺ OT-I cells.

Intra-Tumoral Injection of Hp-91 Peptide Causes Recruitment of T Cellsand Dendritic Cells to the Tumor.

The number of lymphocytes and DCs within tumor has been shown tocorrelate with good prognosis. In certain subsets of breast tumors thepresence of tumor-associated macrophages is associated with betterprognosis. Thus, in order to maximize the anti-tumor immune response wetested two TLR agonists; pI:C (TLR3 agonist) and Pam3Cys (TLR2 agonist),and our immunostimulatory peptides for their ability to recruit immunecells to the tumor. Hp-91, pI:C, or Pam3Cys were injected into B16melanoma, the mice were sacrificed 24 h after the injection and thetumor was frozen and sections stained for the indicated markers.Although all three adjuvants caused recruitment of macrophages (MacI+)into the tumor, only Hp-91 also caused the recruitment of DCs (CD11c+)and T cells (CD3+) (FIG. 23). Further characterization using cell typespecific antibodies, suggests that these are CD8+ cells. No CD4+ T cellsor FoxP3+ cells (Treg) were detected (data not shown). This is a verypromising result as Hp-91 will not only contribute to the recruitment ofDCs, but also mature the arriving DCs. Thus in the context of antigenrelease by concurrent local cytotoxic therapy, we expect to create avery favorable environment for the uptake of tumor antigen by DCs andtheir subsequent activation. In addition, CD8 T cells after being primedin the draining lymph nodes are expected to be recruited in highernumbers to the tumor site via the peptide leading to a strong immuneresponse and tumor killing.

Coupling of Hp91 to DNA-NP

A method to attach peptides to DNA-NP has been developed. The peptide issynthesized as a c-terminal conjugate to a 15 base oligonucleotide thatis complementary to the sequence of the DNA-NP ligation or priming site.A Cy5 labeled Hp91-oligo conjugate was synthesized with a complementarysequence to clone 3. An estimation of the number of potentialhybridization sites on the DNA nanoparticles was made from the total DNAquantitation. The nanoparticles were then hybridized at 37° C. for 30minutes with increasing concentrations of the conjugate. Afterhybridization, the mixture was purified by low pressure size exclusionchromatography for which the elution profiles of the DNA nanoparticlesand the free Cy5 labeled peptide-oligo conjugate had been previouslyestablished. At high ratios of Cy5 peptide-oligo conjugate to DNAnanoparticles, a significant fraction of the conjugate remainedunhybridized as indicated by a strong peak at the free conjugateretention time. As the ratio of the labeled conjugate to the estimatedhybridization sites on the DNA nanoparticles dropped, the free conjugateelution peak began to drop, eventually disappearing at a ratio of 1:2(labeled conjugate:DNA nanoparticle sites) indicating that the DNAnanoparticles can be loaded to saturation by hybridization when 50% oftheir available sites are occupied.

Research Design and Methods

Some embodiments will utilize existing DC binding DNA-NP to find thosethat best stimulate DCs into antigen presenting cells as measured by Tcell activation. If none of the existing particles are sufficient newones can be selected by several strategies or, if that fails, combine DCbinding DNA-NP with the potent peptide adjuvant Hp91. A unique featureof the technology can be exploited to make hybrid particles anddetermine if they offer improved performance over single sequenceparticles. Once the most promising candidate particle is identified itcan be tested in the B16-OVA mouse melanoma model by both intra-tumoraland systemic administration, with and without the model tumor antigen.Initial studies of immune responses can direct pilot studies ofanti-tumor responses, with success leading to larger, statisticallypowered studies.

Methods to Screen DNA-NP that Activate DC.

Five DNA-NP that bind to DC have been identified. These can be comparedfor their ability to activate DC. The DC stimulatory capacity of DNA-NPscan be assessed on myeloid (CD11c+) bone marrow-derived DCs (BM-DCs) invitro, as these are known to function similarly to humanmonocyte-derived DCs.

DC activation and maturation is characterized by altered surfaceexpression of characteristic molecules, production of large amounts ofcytokines and enhanced T cell stimulatory capacity. Therefore, thedendritic cell stimulatory capacity of the DC-binding DNA-NPs can beevaluated in three ways: 1) their ability to alter the expression ofsurface molecules on immature dendritic cells that are classically up ordown regulated upon maturation; 2) their ability to induce secretion ofinflammatory cytokines, and finally 3) their ability to mature DCs intoeffective antigen presenting cells that activate naive antigen-specificT cells. The activity of the DNA-NPs can be compared to PBS (negativecontrol) and LPS as positive control. Bone marrow DCs can be generatedfrom primary mouse bone marrow cells depletion of other cell types andculture with GM-CSF (Inaba K, et al., (1993) Granulocytes, macrophages,and dendritic cells arise from a common major histocompatibility complexclass II-negative progenitor in mouse bone marrow. Proc Natl Acad SciUSA 90: 3038-42). Each DNA-NP can be tested at final concentrations of10 and 100 ng/ml, which corresponds to rough 10⁹ and 10¹⁹ particles perml.

After 48 h, the CD11c⁺ CD11b⁺ B220⁻ myeloid DCs can be analyzed forsurface expression of MHC-II, CD86, CD40, and CD80 by flow cytometry.Furthermore, the cell culture supernatants can be assayed for thecontent of IL-12, IL-6, TNF-α, IL-8, IL-10, TGF-β and IL-1α by ELISA. Todemonstrate functional maturation of DCs stimulated by the DNA-NPs, DCscan be tested for their capacity to activate antigen-specific syngeneicT cells. Bone marrow-derived DCs generated from C57BL6 mice will bestimulated with DNA-NPs, LPS (positive control) or PBS (negativecontrol) for 24 h. The next day the DCs can be pulsed with OVA₂₅₇₋₂₆₄peptides (for CD8 T cells) and OVA₃₂₃₋₃₃₉ (for CD4 T cells) andco-cultured with TCR transgenic OVA-specific OT-I and OT-II transgenic Tcells for 38-50 h. C56BL/6 mice are chosen, because antigen presentationcan be readily monitored using CD4+ and CD8+OVA-specific OT-II and OT-Itransgenic T cells. T cell activation can be assessed for a)proliferation by measuring the uptake of [³H]-thymidine during theremaining 16 h of culture, and b) Th1 and Th2 cytokines by measuringIL-4, IL-2, IL-10 and IFN-γ levels of the cell culture supernatants byELISA and intracellular IL-4, IL-2 and IFN-γ levels by flow cytometry.For intracellular staining of cytokines, the cells can be incubated withbrefeldin A to prevent leakage of the cytokines before permeabilization.

Particle Ranking and Hybrids

The particles can be ranked according to their activity in the assaysherein. Since T cell stimulation is the ultimate goal, significantweight can be given to those results, followed by up-regulation ofco-stimulatory molecules. However, any particle that shows activity inany of the assays can be included in the hybrid particle matrix herein.

As described herein, methods for producing DNA-NP with two or morediscrete sequence components are provided. Individual DC bindingparticles that show activity can be combined to further enhance theirpotency. The counter hypothesis would be that the particles all functionvia the same mechanism and that there will be no advantage to combiningthem. Hybrids pairs can be produced from all sequences that producedpositive results above. If all five of the particles tested showactivity, that would require 10 unique hybrids. These can be assayed andranked as described above. These experiments can be the most interestingif different particles show a different spectrum of activation (ie.cytokine secretion but not phenotypic maturation, T cell stimulation inthe absence of cytokines). However, if none of the hybrids shownsuperior activity to the composite monomers then only the monomers maybe used.

Mechanism

Mechanistic studies are performed to address whether: 1) endocytosis isrequired for the DNA-NP activity, and 2) the DNA-NP activity occurs withTLR/MyD88. The first question is addressed using a panel of endocytosisinhibitors concurrent with DNA-NP, using cytokine secretion andphenotypic maturation as readouts. The inhibitors are brefeldin A andcolchicine, both of which interfere with vesicle trafficking, filipin,which is known to inhibit caveolae-mediated endocytosis by binding tocholesterol and disrupting caveolae structure and function, and sucrose,which generates hyperosmolarity that blocks membrane internalization andclathrin recycling via the coated-pit pathway. Confocal microscopyconfirms the intracellular localization of the DNA-NP.

The potential role of TLR signaling is addressed by using DC from TLR3,4,7, and 9 as well as MyD88 knockout mice. An hypothesis is that theDNA-NP bind to the surface of the DC by some DC specific protein orglycoprotein and are then internalized by endocytosis. While in theendosome they signal through TLR9 and, downstream, MyD88. However, it ispossible that DC activation occurs by other mechanisms and the initialbinding event could trigger MyD88 independent pathways. The rapidcalcium flux would be consistent with this model. These experimentsprovide a basic working model for the DNA-NP activity.

In Vitro Selection Against Mouse DC

A pool of DC binding particles were selected against human DC. While atleast one clone also binds to mouse DC, activation of mouse DC was notconfirmed. Bone marrow-derived DCs are generated from C57BL/6 mice.These bone marrow-derived DCs are generated in the presence of GM-CSFand yield only myeloid not plasmacytoid DCs (PDCs), since GM-CSFprevents the development of PDCs. Further purification are achieved bypositively selecting CD11c⁺ cells from the day 6-8 cultured usingmagnetic beads. If non-specific cell binders are recovered, an adherentmouse fibroblast cell line is used for counter selection. The adherentcells absorb non-specific cell binders and are removed from thenon-adherent DCs.

In Vivo Selection

In vivo selection of targeting ligands has been well established withphage displayed peptide libraries. While seemingly a complicated andpotentially difficult proposition, in vivo selections have twosignificant advantages. The first is that the selection is beingperformed in the very same environment that the ultimate product will beused. The second is that the rest of the animal acts as a subtractivesubstrate that will remove any non-specific particles. We will performin vivo selections by injecting the DNA particle library subcutaneouslyand recovering the draining lymph nodes several hours later. The lymphnodes will be treated with collagenase to create single cellsuspensions, and the MHC-class II+ antigen presenting cells (includingDCs and B cells) will be isolated by magnetic bead separation.Subsequently the particle recovery, re-amplification, and ligation is asdescribed herein.

Combinatorial Library Screening

FIG. 24 shows a strategy for selection and combinatorial breeding ofmultimeric polyvalent DNA nanoparticles. Step 1. Several libraries withunique ligation and PCR primers are generated. Step 2. Each library isindependently screened for a few rounds against the target to create aninitial enriched pool. Step 3. The products of the initial screeningsare combinatorially assembled into multimeric templates and polyvalentDNA particles are generated. Step 4. The particles are subjected tosubtractive screening to enrich the desired binding activity andeliminate unwanted cross-reactivities as described herein. In eachselection step the individual library components are re-assorted,creating additional combinatorial diversity from which optimal particlescan be selected.

The hybrid particle concept can be introduced at the library screeningstep. The specificity of particles for cancer cells can be improved ifmore than one ligand is targeted, creating an “AND” type function forbinding. This can be implemented by performing several selectionsagainst a given target cell population using libraries with differentcircularization and PCR primer sequences. The products of each selectioncan be combinatorially assembled by creating particles that consist ofone unit from each library. In this way particles can be “bred” thatoptimize selectivity and exploit the potential that each DNA unit mightrecognize a distinct component of the target cell. In each round, thethree component pieces are re-assorted so that the optimal combinationenrich over several rounds of selection.

Candidate Particle Cloning and Binding to Target Cells

After a successful selection, candidate particles are further analyzedfrom the final pool. To obtain individual particles, the final pool areamplified by Stoffel PCR and cloned into a plasmid sequencing vector.Once cloned, 10-20 candidates are sequenced to determine the extent ofsequence diversity in the final pool. Each candidate can be re-generatedby PCR/asymmetric PCR amplification from the plasmid. The candidateparticles from a selection are tested individually for target cellbinding by making fluorescently tagged particles. The labeled clones areincubated with lymph node suspension cells on ice for 1 h and co-stainedwith antibodies against B220 (B cells), CD11c (myeloid DCs), and PDCA-1(plasmacytoid DCs) to identify the bound target cells and demonstratespecificity. Labeled cells are analyzed cell binding by flow cytometryand fluorescent microscopy.

Addition of Immunostimulatory Peptide Hp91

If no particle is obtained with the ability to activate DC, the DCbinding DNA-NP is used as a carrier for peptide Hp91 as described in thepreliminary data. It is determine if the DNA-NP/Hp91 formulation retainsor improves the activity of the DC stimulatory activity of the peptide.Even if there is not an improvement with the DNA-NP in the in vitroassays, in vivo experiments are performed as it is possible that theDNA-NP targeting could be far more relevant in the in vivo.

Methods to Test the Hypothesis that Direct Injection of DNA-NP intoTumors Activate Tumor Infiltrating DC

Tumor Model

All in vivo experiments are conducted in a transplantable mouse model ofmelanoma using the mouse melanoma cell line B16-OVA that expresseschicken ovalbumin, which serves as a tumor marker to monitor immuneresponses. When injected s.c. into C57/BL6 mice, B16-OVA produces alocal tumor growth. The experiments are hierarchically designed toreveal that 1) the DC binding DNA-NP can perform that function in vivo,2) that immune activation via DNA-NP within the tumor can awaken a tumorspecific immune response, and 3) that immune response will lead to tumorrejection.

C57/BL6 mice (n=5 per group) are inoculated with 5×10⁵ B16 cells s.c.Once the tumors reach 3-5 mm in size they receive intra-tumoralinjection of: 50 μl of PBS, DC binding DNA-NP, or a control DNA-NP.DNA-NPs is injected at 1 and 10 μg/ml (˜10¹⁰ and 10¹¹ particles)suspended in PBS. 24 hours later the mice are sacrificed and the tumor,draining lymph nodes, blood, liver, and spleen are collected.

Histology is performed on the tumor and the number of infiltratinglymphocytes compared (CD3+ and CD11c+) to controls. Single cellsuspensions are made by treating the tissue with collagenase and theexpression of IL-12, IFNγ, TNF alpha, and RANTES by sorted CD11c+ cellsdetermined by RT-PCR. The particle characteristics are optimized.

Nanoparticle Optimization

The size of the DNA nanoparticles can be tuned by the RCA reaction time(see data herein). The DNA-NP are synthesized under reaction conditionsthat produce a mean size of 100, 200, and 300 nm as measured by dynamiclight scattering. Aliquots are reserved for confirmation by WETSEM (seedata herein for example image). The different size batches are equalizedfor total particle number and compared as described herein. The optimalsize thus determined is used for all other experiments.

In addition, the nuclease sensitivity can be manipulated in severalways. The particles are inherently resistant to exonucleases since theyare a continuous single strand with only one 5′ and one 3′ end.Furthermore, these ends can be made exonuclease resistant. The 5′ end iscreated by the ligation primer and can therefore be made with an alteredbase (e.g. phosphorothioate) at the time of oligonucleotide synthesis.The 3′ end can be made resistant by adding a modified dideoxy nucleotidetriphosphate at the end of the RCA reaction, such that the growingstrands are terminated by an exo resistant base. The particles areinsensitive to endonuclease because of their primarily single strandedcharacter. However, endonuclease resistance can be increased by theincorporation of phosphorothioate nucleotides during the RCA reaction.Furthermore, degradation independently increases activity of CpGoligonucleotides containing phosphorothioate backbones. Particles aresynthesized that contain entirely a phosphorothioate backbone and arecompared as described herein.

Tumor Regression Studies

A long term tumor monitoring study is performed. Groups of mice (n=5)are inoculated with tumor and injected with DNA-NP or controls asdescribed herein. 7-14 days after the initial injection mice receive asecond injection identical to the primary one. The mice are observedbi-weekly and the primary tumor size measured using a set of calipers:A×B²/2 (A=long axis, B=short axis) over a period of 20 days. After 20days or if the tumors reach 1.5 cm in diameter, whichever occurs first,mice are sacrificed. At time of euthanasia mice are monitored forpotential pathological effects. The spleen and kidney are weighed andtissue analysis is performed.

Methods to Test the Hypotheses that Immunization with DNA-NP and ModelTumor Antigens Elicit Antigen Specific Responses and Tumor Rejection

Co-injection of the most potent DNA-NPs identified herein with antigencan lead to the induction of an immune response. The potency of DNA-NPsas vaccine adjuvants is compared to alum to measure the quality as wellas quantity of the immune response by using the same route ofimmunization. Ovalbumin (OVA) and influenza haemagglutinin (HA) havebeen suggested to study the adjuvanticity of new formulations. Sincealuminum compounds do not exhibit an adjuvant effect when used with HA,whole OVA protein are used as antigen, to establish the adjuvanticity ofthe DNA-NP.

The adjuvanticity of the DNA-NPs is assessed and compared to aluminumhydroxide. Groups of C57BL/6 mice (n=10) receive s.c. injections ofOVA/PBS (as negative control), OVA/aluminum hydroxide (Alhydrogel^(R),aluminum hydroxide, from Superfos Biosector, Vedbaek, Denmark) (positivecontrol), or OVA/CpG (positive control), and 3 different doses ofOVA/DNA-NPs (1-100 μg/mouse), that show DC activation in preliminarystudies. Optimal formulations of antigen adsorbed to aluminum adjuvantare prepared to correctly evaluate new adjuvants. To minimize variationand to avoid non-reproducibility due to different preparations ofaluminum components, a specific preparation of Alhydrogel^(R), aluminumhydroxide, from Superfos Biosector, Vedbaek, Denmark, are used. Thecomplete absorption of the antigen on aluminum adjuvant is verified bymeasuring antigen/protein levels before and after adsorption in thesupernatants. The conditions are optimized to reach the WHO recommendedadsorption of 80%. Two to three weeks after immunization the animalsreceive a second “booster” immunization performed exactly as the firstinjections. Blood is obtained from mice at three time points: beforeimmunization for base antibody levels, before the booster immunizationand 1-2 weeks after the second “booster” immunization. Plasma IgG andIgM levels specific for the injected antigen are measured by directELISA using plates coated with antigen. The antibody results aredetermined in arbitrary units against an ELISA reference serum in orderto reliable compare results obtained on different days. The type ofimmune response is further characterized by measuring the subclassantibody concentrations. In mouse, the production of IgG2a is recognizedas characteristic of a Th1 response, whereas the production of IgG1 ischaracteristic of a Th2 response. Therefore, the assessment of the typeof immune response is performed by measuring IgG1, IgG2a and IgG2blevels by ELISA. The ratio of IgG2a/IgG1 antibody titers is used asindicator of Th bias. A Th2 response is also characterized by thesecretion of Th2 type cytokines, such as IL-4, IL-5, whereas a Th1 typeresponse is characterized by the secretion of IL-2 and IFN-γ.

The in vivo induced T cell responses is detected in vitro using avariety of assays. 1) Proliferation assays are performed by addingOVA₂₅₇₋₂₆₄ peptides (to stimulate CD8 T cells) and OVA₃₂₃₋₃₃₉ (tostimulate CD4 T cells), PBS/no peptide (negative control) or ConA(positive control) to un-separated lymph-node cells from the draininglymph node, which contain T cells and antigen presenting cells, andmeasuring the uptake of [³H]-thymidine after 4 d. To measure T cellresponses, un-separated lymph-node cell cultures are set up as describedherein, but the positive control will be phorbal myristate acetate (PMA)and soluble anti-CD3, since ConA is not a potent stimulus for Th2cytokines. After 24 h the culture supernatants are assessed for IL-4,IL-2, IL-5, IL-10, TGF-β and IFN-γ levels by ELISA. IFN-γ ELISPOT andintracellular flow cytometry assays for IL-4, IL-2 and IFN-γ are used tomeasure the number of cytokine secreting T cells and double labeling forCD4 and CD8 to detect the type of T cells responding. For intracellularstaining of cytokines, the cells are incubated with brefeldin A toprevent leakage of the cytokines.

Tumor Rejection Studies

C57/BL6 mice are inoculated with 5×10⁵ B16 cells s.c. Once the tumorsreach 3 mm in size, groups of mice (n=20) receive s.c. immunizations ofOvalbumin mixed with: PBS, or 10 μg DNA-NPs. 7-14 days after the initialinjection mice receive a second injection identical to the primary one.Half the mice from each group (n=10) are sacrificed to analyze immuneresponses and the other half are monitored for tumor progression.

Ten days after the final immunization, half the mice from each group aresacrificed and tumor draining lymph nodes and spleens are harvested.Unfractionated lymph node cells and splenocytes are cultured in mediumonly and re-stimulated with mitomycin C-treated (50 μg/ml) B16-OVAcells. B16-OVA cells are exposed to mitomycin C for 20 min, washed andco-cultured with lymph node cells. As a positive control lymph nodecells and splenocytes are stimulated with Concanavalin A (5 μg/ml).After 16-40 h the cell culture supernatants are assessed for IL-2, IL-4,IL-5, IL-10, TGF-β and IFN-γ levels by multiplex-luminex assay or ELISA.IFN-γ ELISPOT is used to measure the number of cytokine secreting Tcells. To further investigate the contribution of CD8+ and CD4+ T cellsto the cytokine secretion, each cell type is depleted from thesplenocytes separately using specific antibodies prior to in vitroculture. To measure the generation of functional CTL responses,unfractionated lymph node cells and splenocytes are re-stimulated invitro with the mitomycin C-treated (50 μg/ml) B16-OVA cells. The cellsare expanded in 24-well plates for 6 days at a concentration of 3×10⁶cells in 1.0 mL of medium with the addition of recombinant mouse IL-2(50 U/ml) after 24 h of culture. Cytolytic activity is assessed at day 6by culturing expanded lymph node cells and splenocytes with B16-OVAtarget cells and B16 (=negative control target cells), using a standard4 h LDH assay. The absorbance values from supernatants are recorded atOD 490 nm. The percent of specific lysis is calculated as follows:(D_(EXp).−OD_(spon.E)−OD_(Spon.T)/OD_(Max.T).−OD_(Spon.T))×100, whereOD_(Exp) is the OD related to the experimental LDH release, OD_(Spon.E)the OD related to the spontaneous release of LDH from the effector cellsonly, OD_(Spon.T) is the OD related to the spontaneous LDH release fromtarget cells only, and OD_(maxT.) is the OD related to the maximum LDHrelease from target cells using lysis buffer.

The other half of mice from each group (n=5) are observed bi-weekly andthe primary tumor size is measured using a set of calipers: A×B²/2(A=long axis, B=short axis) over a period of 20 days. After 20 days orif the tumors reach 1.5 cm in diameter, whichever occurs first, mice aresacrificed. At time of euthanasia mice will also be monitored forpotential pathological effects see below. The spleen and kidney will beweighed and tissue analysis will be performed by our molecular pathologycore.

If there is a low frequency of melanoma-specific T cells a second roundof in vitro activation of the lymph node cells might be necessary. Cellsare cultured for 12-16 days with periodic re-stimulation of the cultureswith tumor-lysate pulsed irradiated syngeneic BM-DCs. After 2-3 roundsof re-stimulation, the lymph node cells are mixed with target cells andassayed for their killing capacity as described herein. If no specificlysis of target cells is observed in the LDH assay, target cells arepre-treated with 20 ng/ml IFN-γ24 hours prior to use in cytotoxicityassays, which is known to increase the HLA expression. HLA molecules aremonitored by FACS.

Pharmacodynamics and Toxicity of DNA-NPs In Vivo.

The immunization experiments provide an opportunity to gain insight intothe in vivo distribution and half life of the DNA NPs, as well as anyassociated toxicity. Organs and blood are recovered from the sacrificedanimals and tissue extracts prepared. An attractive feature of theDNA-NP is that they can be very sensitively and precisely quantified byreal time PCR. rtPCR is used to surmise the biodistribution andcirculating levels of the particles. DNA-NP were injected into miceintravenously and no ill effects were observed.

Groups of mice receive DNA-NPs, that show activity in the tumor modeldescribed herein, in 3 different doses s.c. (1-100 μg/mouse). All miceare monitored daily for necrotic areas at the site of injection and forsigns of distress and death over the course of all experiment. Any micethat die or are euthanized due to distress or discomfort is evaluated.Furthermore, serum is assayed for anti-nuclear antibodies by standardimmunofluorescence approaches, for anti-DNA antibodies by L. crithidiaassays, and for rheumatoid factor and anti-HMGB1 antibodies by ELISAonce every two weeks until 2-3 months after the injection of adjuvant.At time of euthanasia mice are also be monitored for potentialpathological effects. The spleen and kidney will be weighed and tissueanalysis will be performed.

It is possible that high levels of DNA-NPs could potentially cause sideeffects, such as local tissue necrosis or lead to the induction ofanti-DNA antibodies. If tissue necrosis occurs it will likely be mildand transient, since the DNA-NPs are not administered chronically. Ifside effects occur, lower doses are tested.

Concurrent Cytotoxic Therapy

An hypothesis for antigen agnostic approach is that DNA-NP willstimulate the tumor infiltrating DC which will, in turn, awaken tumorspecific CTLs. However, other immunotherapy studies in this system shave shown improved results when combined with cytotoxic therapy. If theDNA-NP alone do not induce tumor regression, experiments are repeatedwith concurrent treatment using 5-azacytidine(5-aza). 5-aza is giveni.p. at a dose of 0.2 mg/kg for three cycles, each cycle consisting of adaily i.p. injection for 5 consecutive days followed by 2 days rest.

EXAMPLES Example 1 Generation of Nanoparticles

This example demonstrates the characterization of the DNA nanoparticles.Nanoparticles were created through RCA with a variety of differentencoding sequences. Nanoparticles were made into discreet particles asimaged by microscopy (FIG. 25) and were made in varying sizes asdetermined by DNA binding dyes in a flow cytometry setting (FIG. 26).Discreet DNA nanoparticles were made with modified fluorescentnucleotides as an internal labeling method with little to no background.In addition, the DNA binding drug Doxorubicin was loaded on the DNAnanoparticles (FIG. 27).

Example 2 Generation of Aptamer Particle Libraries

Multivalent aptamer containing particles will be generated from circularoligonucleotide templates by rolling circle amplification. FIG. 28 showsthe library template oligonucleotide design. The ends contain PCR primerbinding sites for the amplification of the library during rounds ofselection. These ends also bind to the ligation template oligonucleotideto circularize the template for RCA amplification. The random sequenceis 60 nucleotides long and is flanked by defined sequences that can beused to hybridize fluorescent or otherwise labeled probes forvisualization or purification.

The generative library oligonucleotide templates will be circularized byannealing to a complementary ligation target. That targetoligonucleotide will also serve as the primer to initiate rolling circleamplification (RCA) by phi29 polymerase. RCA produces a single strandedconcatemer that is the complement of the library templateoligonucleotide (FIG. 29, panel A). The number of repeats contained in agiven strand is a function of the size of the template and the amount oftime the RCA reaction is allowed to proceed. Initially, 30 minute to onehour reactions will be used to produce strands containing severalhundred repeats. These strands collapse into random coiled balls thatare 100-1000 nm in diameter. Each particle should have many copies ofthe aptamer on or near the surface of the particle, enabling multivalentinteractions with targets.

Example 3 Screening Aptamer Particle Libraries

The particle library will be panned against touch preparations of breasttissue containing both normal and malignant cells. Slides used will beselected as those with small numbers of clearly identifiable tumor cellsin a background of many normal cells. The normal cells will serve tosponge away aptamer particles that bind to targets found on both normaland tumor cells. Tumor specific aptamer particles will be recovered byeither positive or negative selection using a laser capture microscopy(FIG. 29, panel B).

Example 4 Amplification and Regeneration of Aptamers

Aptamers bound to the target cells will be amplified by real time PCR.The amplified aptamers will then subjected to several rounds ofasymmetric PCR to enrich for the template strand. The templates will bere-circularized using the ligation template from above and RCA used togenerate particles as originally done (FIG. 29, panel C). Multiplerounds of panning will be performed. The real time PCR amplificationwill give a rough quantitative estimate of the number of bound particlesin each round. Successful enrichments will be indicated by a substantialincrease in the number of bound particles (for example, 100-1000 fold).

Once a pool of aptamers has been enriched against the breast tumorcells, individual aptamer sequences will be determined by cloning thefinal amplified products into a plasmid vector and sequencing. Clonalpopulations of aptamer particles derived from individual aptamers can berecreated from these clones by the same PCR/asymmetric PCR approach usedin the screening rounds.

The aptamer particles can be readily labeled either with DNA bindingfluorescent dyes (for example, Sybr gold, or oligreen) or byhybridization of a fluorescently labeled oligonucleotide probe. Theclonal populations will be tested for specific binding to breast tumorcells by fluorescent in situ histochemistry. Individual aptamerparticles stained with a DNA dye such as Oligreen, are sufficientlybright to be detected by a flow cytometer.

Example 5 Development of Multimeric Polyvalent Aptamer Particles

The modular nature of the DNA particles allows for multiple discreteaptamer sequences to be displayed on a given particle. The specificityof particles for cancer cells should be improved if more than one ligandis targeted, creating an “AND” type function for binding. This will beimplemented by performing several selections against a given target cellpopulation using libraries with different circularization and PCR primersequences (FIG. 30). The products of each selection can then becombinatorially assembled by creating particles that consist of one unitfrom each library. In this way we can “breed” particles that optimizeselectivity and exploit the potential that each aptamer unit mightrecognize a distinct library. In each round, the three component pieceswill be resorted so that the optimal combination will enrich overseveral rounds of selection.

Example 6 DNA Nanoparticle Libraries for Imaging and TherapeuticApplications

Rolling Circle Amplification (RCA) of a circular DNA template produces acontinuous single stranded complementary concatemeric nanoparticle.These particles may have applications in biological sensing, detection,and therapeutics. RCA reactions were monitored in realtime and therelationship between reaction times and conditions and particle sizedetermined by dynamic light scattering and gel electrophoresis. DNAbinding fluorescent dyes were used to visual the particles in flowcytometry and fluorescent microscopy. A purification strategy based onsize exclusion chromatography was developed. The nuclease sensitivityprofiles of the particles were determined for both endo and exonucleases: these could be attenuated by the incorporation ofphosphorothioate nucleotides during the RCA reaction or by modifying the5′ or 3′ bases of the strand. The stability of the particles in humanserum and plasma was evaluated and the interactions with serum proteinswas profiled. These experiments lay the foundation for furtherdevelopment of DNA nanoparticles for biomedical applications.

Example 7 Production & Characterization of DNA Particles Incorporationof Phosphorothioate Nucleotides

RCA reactions were run using either dNTPs, a mixture of dNTP andphosphorothioate backbone cytosine nucleotides (CαSTP) at a 1:1 ratiowith dCTP, or with a nucleotide cocktail where all dCTP was replacedwith CαSTP. The results indicate that the phi29 DNA polymerase canincorporate CαSTP in place of dCTP during the RCA process, albeit withsome loss of efficiency (FIG. 31).

Method to Purify the Particles by Size Exclusion Chromatography

Protocol for size exclusion resins: 1. Template circles were RCAed at 1nM in 50 μl volumes for 30 minutes and stopped with 5 μl 500 mM EDTA.Oli Green 1× was included in the reaction. 2. EconoColumns (BioRad) 0.5cm internal diameter×5 cm length were filled with Bio-Gel P-100 MediumResin (90-180 μm hydrated radius, fraction range 5-100 kDa). The resinwas hydrated in PBS and was packed to a column height of 3.7 cm, totalcolumn volume 726 μl. PBS elution buffer was drained to the top of thecolumn and 50 μl of sample was applied and 1 drop was released from thebottom of the column to let sample enter resin—column was then closed. 1mL of PBS was added to provide hydrostatic pressure (this was keptconstant as column flowed) and drops were collected on full flow rate.Drops were then measured for A260 and Ex 480 Em 520 showing clearfractionation between nucleotides and DNA created (FIG. 32).

Method to Purify Small Volumes of Particles by Drop Dialysis &Centrifugal Concentration

Protocol for drop dialysis: 1. RCA products were made at 1 nM in 100 μlwith ligations from the streptavidin padlock probe for 5, 10, 30 and 60minutes respectively and stopped with 10 μl 500 mM EDTA. 2. ThreeMillipore MF membranes 0.05 μm VMWP (2.5 cm) were floated on 100 mL TBSin a glass dish until hydrated. 30 μl from each time point was appliedfor each time point. 20 μl of each sample was recovered at theappropriate time point. Time points were 30, 60, and 120 minutes. A zerotime point was not applied but kept aside. 3.10 μl of each recoveredsample from each time point was mixed with 40 μl TBS and 0.125 (1×)stock Oli Green and measured at ex 480 em 520.

FIG. 33 shows a drop dialysis recording of 30 minute unlabelled RCAreaction (normal dNTPs) along side a different drop containing Alexa-488nucleotides. Every hour 1 μl of each drop was removed and diluted in 50μl PBS and measured. The Alexa-488 nucleotides were measured by simplefluorescence and the DNA was measured by Oli Green.

DNA particles were cleaned with centricon YM-30 column at differentspeed. Speed 14,000 rpm and 5,000 rpm gave similar amount of flowthrough, but 1,000 rpm did not seem sufficient to drive the liquidthrough the membrane in a reasonable time (FIG. 35).

Method for DNAse and Exonuclease Resistance Profiles

Step 1. Template circles were RCAed at 1 nM using phosphodiester dNTPsfor 10 min at 30° C. and heat inactivated at 65° C. for 10 min. Step 2.RCA products were mixed 1:1 with 1×NEB buffer 2 containing 2× OliGreenstock dye. Step 3. Similarly, ss probe (unligated linear templates) wasdiluted to 100 nM in phi29 buffer and mixed 1:1 with 1×NEB buffer 2containing 2× OliGreen. Step 4. Each sample was divided into 3 equalaliquots of 100 μl and each aliquot received either 20 units Exonuclease1 or nothing. Samples were monitored by Ex 480 Em 520 at 37° C. over 1hour with 20 second interval reads. Step 5. Percent digestion iscalculated as the 1-(the ratio of the digested signal to blank signal).Step 6. RecJ may not be optimal. Also note that the ExoI digestion wasalready very progressed by the time readings started (FIG. 36).

More experiments to characterize DNA particles include experiments whereserum stability and interactions are tested. The incorporation ofnucleotides with free carboxy, thiol, amine for conjugating other smallmolecules is tested. Incorporation of biotinylated nucleotides istested. Attenuation of nuclease sensitivity by incorporation of modifiedDNA or RNA backbones is tested.

Labeled with DNA Binding Dye (Oligreen) by Flow Cytometry & Microscopy

DNA particles were made by RCA reactions of varying times, labeled withOligreen dye, and run on a flow cytometer. The fluorescence intensitycorrelates with the length of the reaction and presumably the size ofthe particles (FIG. 37).

DNA nanoparticles visualized with Sybr Green dye (FIG. 38). LEFT: 100×of 30 min RCA, RIGHT: 100×90 min RCA. Particle density is dependent onthe spot and the time it has been under the light (photo-bleachingoccurs).

Labeled with Incorporated Fluorescent Nucleotides or Hybridized Probe byFlow Cytometry.

This is an example of Alexa-488 labelled DNA balls. The experiment wasto hybridize on Alexa-647 oligos and see dual fluorescence. Sample 1 wasthe non labelled DNA with no oligo. Sample 3 was Alexa-488 labelled DNAhybridized to Alexa-647 tagged oligo. The incorporated Alexa 488fluorescence is shown in FIG. 39, while the hybridized probefluorescence is shown in FIG. 40.

Size Distribution by Dynamic Light Scattering

A Zetasizer Nano instrument was used to measure the size distribution ofDNA nanoparticles produced by RCA reactions of varying time, usingdynamic light scattering (FIG. 41). We have noticed in other batchesthat the size seems to peak around 250 nm, even with longer reactiontimes. It is suspected that the size of the particles may be limited bythe processitivity of the phi29 enzyme. Dynamic light scattering mayalso underestimate size due to the low index of refraction of theparticles.

Agarose Gel Electrophoresis

RCA reactions were run for time points 30 sec, 1 min, 2 min, 5 min, 10min across left to right from the 1 kb ladder (FIG. 42). The top band onthe ladder is 10 kb. The RCA reactions were stopped on time by EDTA andthen mixed with alkaline denaturing buffer. They were then heated to 95°C. for 5 min. The gel was a 0.7% agarose alkaline gel. Samples were runfor 3 hours at 40 V and stained with GelRed. The products (including theladder) should be rendered single stranded by the alkaline conditions.

In more experiments to visualize DNA nanoparticles, nanoparticles arevisualized using electron microscopy.

Example 8 Generating a DNA Particle Library Methods to Produce, Select,Amplify, and Reproduce DNA Particles

An overview of the strategy is shown in FIG. 6. (A) LIGATION: (1)Prepare the buffer and add the library and the gluing primer (gp). (2)Boil a water bath, mix solution well and place in water bath. Allowwater to cool to RT slowly. (3) Once about 33° C., add 1 μl T4 ligaseand ligate at RT for 1 hour. TABLE 1 summarizes components of thereaction.

TABLE 1 Component Volume buffer Water 41.5 μl T4 ligase 10 X buffer   5μl 500 mM DTT  0.5 μl Total:   47 μl 10 uM library  0.5 μl 10 uM gp  1.5μl T4 ligase   1 μl

(B) VERIFICATION OF THE RINGS (RCA): (1) Add 49 μl of the master mixwith oh green and add 0.5 μl of ligated sample. (2) Ensure that theTECAN is at 30° C. and add 0.5 μl phi 29 polymerase. (3) Mix togetherand run in TECAN with program 3 Hour RCA FAM to visualize linearamplification—note slope of curve. (4) Run a reference sample with: 0.5μl sal inv pp (Standard for RCA). TABLE 2 summarizes components of thereaction.

TABLE 2 Component Volume Water  40.5 μl   101 μl 413.1 μl 10 X phibuffer    5 μl  12.5 μl   51 μl dNTPs 10 mM    3 μl  7.5 μl  30.6 μl 500mM DTT  0.5 μl  1.25 μl  5.1 μl Oli Green from stock 0.125 μl 0.313 μl10.2 Ligated sample (1 nM)  0.5 μl Phi29 polimerase  0.5 μl

(C) CREATION OF DNA BALLS: (1) Add to the 49 μl of the Master Mix 0.5 μlof ligated sample. (2) Right before starting the program add 0.5 μl phi29 polymerase. (3) Run all tubes at 30° C. for 30 minutes. (4) Stop thereactions with 5 μl 500 mM EDTA—Mix well and store at 4° C. TABLE 3summarizes components of the reaction.

TABLE 3 Component Volume PCR water 40.5 μl 101.25 μl 141.75 μl 413.1 μl10 X phi buffer   5 μl  12.5 μl  17.5 μl   51 μl dNTPs 10 mM   3 μl  7.5 μl  10.5 μl  30.6 μl 500 mM DTT  0.5 μl  1.25 μl  1.75 μl  5.1 μlLigated sample  0.5 μl Phi29 polimerase  0.5 μl

(D) ELISA WELLS: (1) Rinse the Elisa well 2 times with TBS-Tween and 2times with TBS. (2) Add the solution (˜55 μl) in the well and incubatefor 20 min in a shaker. (3) Rinse 3 times with TBS-Tween and 3 timeswith TBS. (4) Elute with 26.6 μl of 0.04% biotin in DI-Water. (5) Let itrest in a shaker for 20 min. The 55 μl can be divided into two parts andselect with those. This decreases the risk of loosing some of thepositive samples. In addition the two parts can be taken along and atthe end, at the PCR cleaning, be re-combined again.

(E) PCR: (1) Take the 26.5 μl of the selected RCA and add 22 μl of PCRmmx and 1 μl of VB and VF; (2) Add 0.5 μl of Stoffel enzyme. (3)Program: Open SYBR Green with Dissociation curve protocol. Select thecorrect wells that your samples. Thermal profile: START: 120 sec at 95°C.; CYCLES: 35 cycles, 30 sec at 95° C., 60 sec at 61° C., 20 sec at 72°C. END: 60 sec at 95° C., 30 sec at 55° C., 30 sec at 95° C. (4) Remove25 μl from each tube and store in new tubes to be run in a gel foranalysis—use a 1.5% precast Gel Red agarose gel run at 115 V for 1 hr.(5) Remove 15 μl from each of the two remaining and transfer to a newtube and store at −20° C. for future reference. (6) Put aside 10 μl ofthe solution for the asymmetric PCR. TABLE 4 summarizes components ofthe reaction.

TABLE 4 Component Volume PCR Water 26.5 μl 66.25 μl 92.75 μl 278.25 μlStoffel 10 X Buffer   5 μl  12.5 μl  17.5 μl  52.5 μl 10 mM dNTPs   5 μl 12.5 μl  17.5 μl  52.5 μl 25 mM MgCl₂   10 μl   25 μl   35 μl   105 μl100 X SYBR (final conc 2X)   1 μl  2.5 μl  3.5 μl  10.5 μl 10 μM vB (200nM final conc)   1 μl  2.5 μl  3.5 μl  10.5 μl 10 μM vF protected Phos  1 μl  2.5 μl  3.5 μl  10.5 μl Stoffel Fragment  0.5 μl

(F) GEL: Create gel: 100 mL 0.5×TBE buffer, 2.5 g Agarose. Boil: 60 secMIX, 30 sec MIX, 10-30 sec and mix until liquid. Add 10 μl of 10000×GelRed dye. Pour gel (˜50 mL) on the tray and add the comb. Let it cool(˜20-30 min) Only once cooled remove the comb. Solutions for the gel: 15μl sample. 6 μl diluted dye. (160 μl water+40 μl of Bluejuice 10× and 40μl Bluejuice 10×). Run 1.5 μl only for the ladder (100 bp) vs the 20 μltotal of sample w/dye. Load a bit of 0.5 TBE buffer on the platform, addthe gel in the tray and cover it with buffer. Run at 70V for 80 min

(G) ASSYMMETRIC PCR: Mix together 10 μl of the PCR product with 37.5 μlof a PCR mmx and 2 μl of VF protected phosphate. Add 0.5 μl of StoffelFragment, flick and put in the machine. Program: Start: 120 sec @ 94°C.; Cycles: 10 cycles, 30 sec at 94° C., 60 sec at 61° C., 20 sec at 72°C. Rest: 4° C. After the asymmetric PCR, PCR clean each sample. TABLE 5summarizes components of the reaction

TABLE 5 Component Volume PCR water 21.5 μl 53.75 μl 225.75 μl 10XStoffel Buffer   4 μl   10 μl    42 μl dNTP 10 mM (2.5 mM ea)   4 μl  10 μl    42 μl MgCl₂ (25 mM)   8 μl   20 μl    84 μl vF protected phos(final conc. 400 nM)   2 μl    5 μl PCR product   10 μl Stoffel fragment 0.5 μl

(H) LIGATION 2 and after: To the cleaned sample add 5 μl of T4 ligase10× buffer, 0.5 μl of 500 mM DTT and 1.5 μl of gluing primer added T.Boil water and place mix in water and allow to cool to RT. Add 1 μl T4Ligase and ligate for 1 hour.

(I) VERIFICATION OF THE RINGS considerations from round 2 on (RCA):Ligation2Slope/slope standard=x. Ligation3Slope/slope standard=y. To getback to the same concentration you need to dilute: 100 x/yμL of ligatedsample over 100 μl of DI water.

(J) ELISA WELL consideration from round 2 on: If the sample on the PCRspikes too early, try to dilute it. After run 2 or 3 run the RCA in anempty container to see eventual non-specific binding.

Example 9 Selection Against a Cellular Target (Primary Human DendriticCells)

Procedure: 1. Count 105 cells to use in 1 mL. 2. Spin 3 min at 3000 rpmremove supernatant and add 50 μl of RCA. 3. Let react for 1 hr on ICE.4. At the same time put 1.2 mL of Cell media on as many eppendorf as theplanned rinses steps and keep it in the ice box. 5. Spin the cells 3 minat 3000 rpm. 6. Remove the supernatant and rinse with 500 μl of COLD 5%BSA in PBS. 7. Remove the cell media from one of the test tube and addthe liquid with the cells. 8. Discard the empty tube. 9. Repeat it asmany times as your rinses steps. 10. Remove the supernatant and add 50μl of Hypotonic Lysis buffer and 3 μl of Proteinase K (10 mg/mL). 11.Put in heat block at 56° C. for 1 hr. 12. Move to a second heat block inorder to stop the protease at 95° C. for 15 min 13. The sample is readyto be used.

Results of a selection against dendritic cells (DC). The final pool ofparticles after 7 rounds of selection by the procedure above was labeledwith alexa nucleotides and added to dendritic cells (green line). Anirrelevant particle was used as a control (blue line). The red line isthe cells alone. The shift in fluorescence, as measured by flowcytometry, indicates enrichment of DC binding particles. The pool ofparticles was cloned into a plasmid vector and individual clonesselected, sequenced, and regenerated by PCR, ligation, and RCA to createindividual clonal particle populations. These were then assayed asabove. FIG. 43A shows an example of a cloned particle (shaded) with highaffinity for DC as compared to a control particle (red) or unstainedcells (blue and grey).

The same clonal particle was assayed against the MDA-MB-231 breastcancer cell line (FIG. 43B).

The particle originally selected against DC does not seem to bind thebreast cancer cell line, suggesting that some level of cell specificitymay have been achieved even without a counter selection strategy., Thisexample shows selection resulting in unique sequence particles that bindto the cells much better than control particles

In more experiments to select against a cellular target (primary humandendritic cells), resulting in unique sequence particles that bind tothe cells much better than control particles the following experimentsare carried out: Selective enrichment of particles that bind to one celltype preferentially over another is performed. In vivo selection fortumor targeting particles in a mouse model is carried out. Multi-librarycombinatorial selection is carried out. Selection for enzymatic activityis carried out.

Example 10 Functional experiments Loading of Doxorubicin into DNAParticles

The fluorescence of doxorubicin is quenched with the addition of DNAnanoparticles, indicating doxorubicin binding to the particles (FIG.44).

Protection of Cells from Dox when Untargeted Particle is Used

The IC₅₀ was determined to be 0.1 μg of Doxo for 104 cells. When thisamount of Doxo is incubated with the DNA particles, the survival isalmost 100%, indicating that DNA absorbed the Doxo and protect cellsfrom the toxicity of Doxo. This preliminary data indicate two things:(1) DNA is not able to get into the cells by itself. Targeted DNAparticles may be selected or a targeting moiety added. (2) At the sametime, DNA nanoparticles absorbed Doxo, which is good for our purpose ofloading DNA with drugs (FIG. 45).

Lack of Non-Specific Activation of Immune Cells with UntargetedParticles

DNA nanoparticles containing an immunogenic CpG sequence were incubatedwith PBMCs and IgM secretion measured. The K3 oligonucleotide is apositive control and contains the same stimulatory sequence as the DNAnanoparticles. “DNA” in the FIG. 46 refers to the nanoparticles. Theexperiments were conducted in both primary serum and heat inactivatedserum.

In more experiments to demonstrate function of DNA nanoparticles thefollowing experiments are carried out Immune activation by targetedparticle containing CpG motifs is performed Immune activation bytargeted particle hybridized to an immuno-stimulatory peptide isperformed Immune activation by chemical conjugation of a TLR3 agonist isperformed Immune activation by combinations of the above is performed.Cell targeting by hybridization of a targeted peptide is performed.

Example 11 Applications: Therapeutic

In experiments to demonstrate therapeutic applications of DNAnanoparticles the following experiments are carried out. Cancer therapyby targeted delivery of doxorubicin is performed. Cancer therapy byimmune activation is performed. Cancer therapy by direct killing oftumor cells is performed. Vaccine adjuvant for protective vaccines isperformed.

Example 12 Applications: Imaging

In experiments to demonstrate imaging applications of DNA nanoparticlesthe following experiments are carried out. Ex vivo imaging of cancercells with tumor specific particles fluorescently labeled orbiotinylated for histochemistry is performed. In vivo imaging withparticles that hold contrast agents is performed.

Example 13 DeNAno: Selectable Deoxyribonucleic Acid NanoparticleLibraries

DNA nanoparticles of approximately 250 nm were produced by rollingcircle replication of circular oligonucleotide templates which resultsin highly condensed DNA particulates presenting concatemeric sequencerepeats. Using templates containing randomized sequences, high diversitylibraries of particles were produced. A biopanning method thatiteratively screens for binding and uses PCR to recover selectedparticles was developed. The initial application of this technique wasthe selection of particles that bound to human dendritic cells (DCs).Following 9 rounds of selection the population of particles was enrichedfor particles that bound DCs, and individual binding clones wereisolated and confirmed by flow cytometry and microscopy. This process,which has been termed DeNAno, represents a novel library technology akinto aptamer and phage display, but unique in that the selected moiety isa multivalent nanoparticle whose activity is intrinsic to its sequence.Cell targeted DNA nanoparticles may have applications in cell imaging,cell sorting, and cancer therapy.

The paradigm of nanotechnology for applications in the medical field hasbeen oriented around the framework of bottom-up construction. Generally,a scaffold of polymer or metal serves as a basis for the addition offunctional moieties to lend the nanomaterial the desired capabilitiessuch as selective targeting, transport of therapeutic and imagingagents, and immune evasion (Ferrari, M. Cancer nanotechnology:opportunities and challenges. Nat Rev Cancer 5, 161-171 (2005)). Whenbiopolymers such as DNA are used, they are often rationally designed toform a predetermined structure (Zhang, C. et al. Conformationalflexibility facilitates self-assembly of complex DNA nanostructures.Proc Natl Acad Sci USA 105, 10665-10669 (2008)). However, this approachhas overlooked a powerful tool of molecular biology: the simple creationand efficient combing of libraries with diversity of 10⁹ or more(Wilson, D. S. & Szostak, J. W. In vitro selection of functional nucleicacids. Annu. Rev. Biochem. 68, 611-647 (1999); Smith, G. P. & Scott, J.K. Libraries of peptides and proteins displayed on filamentous phage.Methods Enzymol. 217, 228-257 (1993); Clackson, T., Hoogenboom, H. R.,Griffiths, A. D. & Winter, G. Making antibody fragments using phagedisplay libraries. Nature 352, 624-628 (1991)). Small nucleic acidaptamer sequences have been identified with binding and enzymaticproperties, but their use in nanoparticle based applications has mostlyinvolved grafting them onto other materials (Tuerk, C. & Gold, L.Systematic evolution of ligands by exponential enrichment: RNA ligandsto bacteriophage T4 DNA polymerase. Science 249, 505-510 (1990);Ellington, A. D. & Szostak, J. W. In vitro selection of RNA moleculesthat bind specific ligands. Nature 346, 818-822 (1990); Bartel, D. P. &Szostak, J. W. Isolation of new ribozymes from a large pool of randomsequences [see comment]. Science 261, 1411-1418 (1993); Huang, C. C.,Huang, Y. F., Cao, Z., Tan, W. & Chang, H. T. Aptamer-modified goldnanoparticles for colorimetric determination of platelet-derived growthfactors and their receptors. Anal. Chem. 77, 5735-5741 (2005)). In thisstudy, the concepts of diverse library selection methods withnanoparticles have been have fused by creating libraries of DNAnanoparticles by rolling circle replication of randomized circulartemplates and selecting for particles that bind to a target cell type.

Rolling circle replication of a circular oligonucleotide template usinga strand displacing DNA polymerase produces a continuous single strandof DNA that is the concatemeric complement of the template. The singlestrand condenses into a discrete particle that can be visualized byfluorescent microscopy and flow cytometry if fluorescently labeled (FIG.47) (Blab, G. A., Schmidt, T. & Nilsson, M. Homogeneous detection ofsingle rolling circle replication products. Anal. Chem. 76, 495-498(2004); Jarvius, J. et al. Digital quantification using amplifiedsingle-molecule detection. Nat Methods 3, 725-727 (2006); Larsson, C. etal. In situ genotyping individual DNA molecules by target-primedrolling-circle amplification of padlock probes. Nat Methods 1, 227-232(2004)).

The processivity of the strand displacing enzyme most commonly used,phi29 DNA polymerase, is ˜60 kb so that a particle produced from a100-200 oligonucleotide template will consist of several hundredcomplementary copies. The size of the particles is a function of thereaction kinetics and can be controlled by stopping the reaction withsaturating amounts of EDTA and/or heat in activation of the polymerase.Dynamic light scattering (DLS) estimates that particles produced fromreactions of 10-60 minutes have hydrodynamic radii between 217-338 nmwith polydispersity indices of 0.228-0.333 (FIG. 8). These measurementsare in good agreement with a freely joined chain model of polymercondensation which estimates a 60 kb ssDNA strand to have a hydrodynamicradius of 379 nm (Austin, R. Nanopores: The art of sucking spaghetti.Nat Mater 2, 567-568 (2003)). Because of their large size and chaoticsingle stranded structure, the particles will not migrate in an agarosegel.

The library screening process consists of three major steps which areperformed iteratively: particle synthesis, selection, and amplification.A random library template sequence(5′-Phos-GCGCGGTACATTTGCTGGACTA-N₆₀-TGGAGGTTGGGGATTTGATGTTG 3; SEQ IDNO:13) (Integrated DNA Technologies, Coralville, Iowa) was circularizedwith a template sequence (TCC AGC AAA TGT ACC GCG CCA ACA TCA AAT CCCCAA CCT; SEQ ID NO:14) using T4 DNA ligase (New England BioLabs,Ipswich, Mass.) and polymerized with phi29 DNA polymerase (NEB) for 30minutes at 30° C. and terminated by addition of 50 mM EDTA. The initiallibrary particle synthesis reaction produced over 10¹⁰ uniquenanoparticles and was used to begin a selection directed against primaryhuman dendritic cells with an eye towards vaccine or cancerimmunotherapy applications (Fong, L. & Engleman, E. G. Dendritic cellsin cancer immunotherapy. Annu Rev Immunol 18, 245-273 (2000)). Boundparticles were amplified by PCR using primers that bound to thesequences flanking the random region. Because each particle containsseveral hundred copies of the sequence unit, PCR amplification from asingle particle is robust. To regenerate the library, the desired singlestrand template was enriched after symmetric PCR by adding a 20 foldexcess of the desired strand's phosphorylated primer v6F (5′-Phos-GCGCGG TAC ATT TGC TGG ACT A; SEQ ID NO:15). The regenerated single strandswere then circularized to form a pool of template circles for the nextround of particle synthesis and selection (FIG. 4). Briefly, DNAnanoparticle iterative selection scheme. ssDNA libraries are ligatedwith T4 ligase and polymerized with phi29 DNA polymerase. 3′-5′exonuclease activity of phi29 DNA polymerase ensures nanoparticle purityfrom extraneous DNA. Immature DCs were cultured in RPMI 1640 mediumsupplemented with 2 mM L-glutamine, 50 mM 2-mercaptoethanol, 10 mMHEPES, penicillin (100 U/mL), streptomycin (100 mg/mL), 5% human ABserum, 1000 U GM-CSF/mL and 200 U IL-4/mL and harvested in days 5-7.Cell incubation and washing followed by QPCR (200 nM primers, 95° C. 2min, cycle 95° C. 30 sec, 61° C. 1 min, 72° C. 20 sec to completion. 5μL of resultant reaction was added to 45 μL fresh PCR buffer with 400 nMphosphorlyated template primer v6F. 10 additional cycles of PCR generatean excess of the desired single strand. DNA was purified with a QIAquickNucleotide Removal Kit (Qiagen, Valencia, Calif.), eluted into T4 DNALigase Buffer and recircularized to begin the next round. Nine roundswere produced after which sequences were cloned using a pGEM-T cloningkit (Promega, Madison, Wis.).

After nine rounds of selection the pool of selected sequences served astemplates for the generation of fluorescent DNA nanoparticles byreplacing 10% of total dCTPs with ChromaTide® Alexa Fluor®488-7-OBEA-dCTP (Invitrogen, Carlsbad, Calif.) in the polymerizationreaction and incubating for 30 minutes at 30° C. followed byinactivation by EDTA. These fluorescent nanoparticles were used in allanalyses of binding by flow cytometry and microscopy. An increase intotal population fluorescence was observed compared to a negative DNAnanoparticle control, suggesting that cell binding particles had becomeenriched (FIG. 49).

Individual population members were cloned, sequenced, regenerated asfluorescent particles, and similarly tested for binding by flowcytometry. Several clones were found to bind to DCs more than anirrelevant particle control with some of them demonstrating similarbinding patterns. The multivalent binding nature of these nanoparticlesmay lend them the ability to bind a pattern of surface markers on a cellsurface rather than a single target. In the four clones tested in FIG.3, there is definitive homology in the binding characteristics of Clones3 and 4 that differs significantly from Clones 10 and 12. It is possiblethat subpopulations of nanoparticles have been selected that bind tounique but distinctive cell surface patterns. It is also interesting tonote that even among clones that exhibited similar binding patterns byflow, there was no obvious primary sequence homology. The shape space ofsuch long concatemers is enormous and it likely that even divergentprimary sequences may accommodate similar cell surface targets.Consequently, a single clone

(Clone 3; SEQ ID NO: 01)(5′-GCGCGGTACATTTGCTGGACTATGCATGTTCGTAGTTATATAGGGGGATTGTTTGATAGTCGGAACCGCTGTGCTCAAAGTTTGGAGGTTGGGG ATTTGATGTTG-3′)was pursued for additional validation (primer sites underlined).Particles with the sequence of Clone 3 were independently generated froma synthetic oligonucleotide template for all subsequent experiments. Acontrol particle made from the reverse complement of the Clone 3template was also produced. While the selection scheme used did notinclude a subtractive or counter-selective step to exclude generic cellbinding, the selected DNA nanoparticles bound only to DCs and not tohuman THP1 (acute monocytic leukemia) and mouse P815 (mastocytoma) celllines (FIG. 50).

Both flow cytometry and fluorescent microscopy supported the conclusionthat the selected particles bind to DCs specifically while the reversecomplement control particle did not. Other cell types tested includingK562 (chronic myelogenous leukemia) and primary CLL cells (chroniclymphocytic leukemia) also showed no difference between control andselected nanoparticles (data not shown). Cell binding could becompletely abrogated by incubation of the nanoparticles witholigonucleotides that hybridize to the selected random regions, thoughhybridizing a smaller oligonucleotide to the flanking sequence did notaffect the DC binding (data not shown). This suggests that the bindingis a consequence of the single stranded nature of the particle,presumably due to specific secondary structure. It is important to notethat the DC specificity that we observed was an inadvertent result thatcannot be assumed in most positive selection mechanisms. Both the powerand weakness of random library selections against complex targets suchas cells is that the binding target need not be known in advance sothere is no reason to believe that any selected ligand would bind atarget unique to a particular cell type. However, subtractive orcounter-selective screens against non-specific cell types can be used ifnecessary to enrich for cell specificity.

An important component of many biological nanoparticle applications forin vivo use is the ability to selectively target the desired cells ortissue. Monoclonal antibodies are the primary tool for biomolecularrecognition both experimentally and in vivo. However, the generalimmunogenicity of non-human antibodies and the immune clearance ofnanoparticle aggregated humanized antibodies raise concerns about thisapproach with nanoparticles. As a result, many nanoparticle applicationshave turned to molecular selection of aptamers and peptides fortargeting ligands in place of antibodies. However, since each of thesemethods produces a small affinity ligand, the transition to amultivalent platform is commonly performed by the relatively crudemethod of simply attaching several monomers to a common surface,assuming the coupling can be performed without losing the bindingactivity of each monomer ligand. A potential problem with this approachis that weak non-specific binding can gain sufficient avidity to dilutethe desired specificity. In contrast, because DNA nanoparticlesdescribed herein are composed of concatemeric repeats of a sequence theyoffer a native multivalent platform in a single particle that allows usto perform a selection on whole particles in the same context ofultimate usage.

DNA has a unique complement of overlapping biochemical, structural, andfunctional activities when compared to other polymers typically used innanoparticle synthesis. DNA motifs can act as ligands to specificbiomolecules, DNA can be immunogenic if it contains unmethylated CpGmotifs, it can act as a scaffold for hybridizing other oligonucleotideconjugates, it can have enzymatic activity, it is easily chemicallymodified to allow small molecule or metal ion attachment and metals canbe directly deposited onto DNA for imagining, and it can carry DNAbinding drugs (Klinman, D. M. Adjuvant activity of CpGoligodeoxynucleotides. Int. Rev. Immunol. 25, 135-154 (2006); Breaker,R. R. & Joyce, G. F. A DNA enzyme that cleaves RNA. Chem. Biol. 1,223-229 (1994); Bern, L., Alessandrini, A. & Facci, P. DNA-TemplatedPhotoinduced Silver Deposition J. Am. Chem. Soc 127, 11216-11217(2005)). DNA has a long clinical history and a favorable toxicity andbiodegradability profile (Fichou, Y. & Ferec, C. The potential ofoligonucleotides for therapeutic applications. Trends Biotechnol 24,563-570 (2006)). Cell specific DNA nanoparticles are a potentialaffinity reagent for research work and are an attractive platform fortargeted imaging or therapeutic applications.

Example 14 ssDNA-Nanoparticles as Molecular Marker for Detection ofCancer Cells

Cancer cells have molecular alterations that can be used for theiridentification at early stages of the disease. ssDNA-nanoparticles aredesigned able to bind to these cell alterations. These particles can becreated by rolling cycle amplification (RCA) from a template DNA.Different DNA templates can be combined together to create a multivalentDNA nanoparticle able to recognize more than one alteration. Startingfrom a random DNA-library, MDAMB-231 cells (epithelial breast cancercell) were incubated with DNA-sequences for several biopanning cycles toenrich the binding sequences. After donning and sequencing of themotifs, these were incubated with 3 different cell lines (2 breastcancer cell lines, MDA-MB-231 and MCF-7, and one monocytic cell line,THP-1) to test the specificity of the ssDNA-nanoparticles. Forty cloneshave been analyzed and at least 2 of them are candidates for specificbinding to MDA-MB-231. These methods and ssDNA nanoparticles are usefulin breast cancer and other types of cancers, for example, lung,pancreatic, brain. The ssDNA nanoparticles contribute to the developmentof new tumor markers and help to consolidate the use of a newtechnology, Nano-technology, for diagnosis of cancer.

FIG. 51. Generation of ssDNA nano-particles: ♦(upper line):cells+qPCR+RCA; ▪: cells+qPCR reagent; ▴: cells+qPCR+RCA(−); ♦(lowerline): cells. A graph of fluorescence (R) vs. number of cycles. Eightbio-panning cycles have been made starting from a random DNA-library. Ineach bio-panning cycle, MDA-MB-231 cells (epithelial breast cancercells) were incubated with ssDNA nanoparticles and the binding particleswere amplified by qPCR. The goal of each cycle was to enrich andamplified the binding motifs.

FIG. 52. DNA gel of amplified sequences: After each bio-panning cycle,the amplified samples were run in a DNA gel where the amplified productscan be visualized. In all the bio-panning cycles, amplified productswere observed only from the samples corresponding to cells+RCA particles(lane 5). No amplification of cell DNA was observed (lane 2, 3 and 4).Line 1 represents the molecular weight ladder.

FACS analysis of the binding ss-DNA nanoparticles to test specificity ofthe particles are shown in FIG. 53-55. ss-DNA nanoparticles weregenerated by RCA and incubated with 3 different cell lines: Twoepithelial breast cancer cells, MDA-MB-231 (FIG. 53A-53C) and MCF-7(FIG. 54A-54C), and a monocytic cell line, THP-1 (FIG. 55A-55C). Thistest was repeated five times. Of 40 clones analyzed, 2 of them, L5C22and L5c37, were specific for MDA-MB-231 cells as is shown in the FACSplots (blue line, background ((−)RCA); red line, specific signal). Thelast column represents the average of the results of five experiments.

Example 15 Bi-Specific DNA-Nanoparticles

This example illustrates the production bi-specific DNA-nanoparticles(NP) that bind to both tumor cells and T cells. Binding particles thatbind the pancreatic tumor cell line, panc02, are used as the tumorbinding moiety. In this example, T cell binding DNA-NP are selectedusing a DNA-NP library technique to identify DNA-NP that bind to mouseand human T cells. Each moiety is selected against separately. Constructand validate Hybrid particle that bind to T cells and pancreatic cancercells are constructed and validated. In addition, the effects ofbi-specific DNA-NP on tumor growth and metastasis are evaluated. Thescheme is summarized in FIG. 56.

DNA-NP differ from other affinity reagents in several ways. Eachparticle contains many copies of the sequence elements so there isintrinsic multivalent display of the modules, allowing avidity tocompensate for low monovalent affinity. Molecular modeling suggests thatthe repeating units that make up a particle can adopt more complexsecondary structures than simply repeating the predicted structure ofthe monomer. The modular nature of the particle template constructionallows multiple distinct recognition elements to be assembled into asingle molecular entity. Furthermore, the selection method allows theoptimal particle to be evolved in the same molecular context in which itwill be used, rather than transplanting them to some other framework orparticle for application.

DNA-NP are produced using methods described herein. Briefly, DNA-NP areproduced by enzymatic DNA synthesis using a strand displacing DNApolymerase, phi29, and a circular oligonucleotide template. Theresulting RCA products are concatemers complementary to the templatecircular oligonucleotide. These long single stranded products collapseinto randomly coiled nanoparticles. DNA-NP can be readily analyzed byDynamic Light Scattering (DLS) and a low polydispersity index. A typical30 minute reaction produces particles ˜250 nm in size, with an estimatedDNA length of ˜30 kb.

DNA nanoparticle libraries are constructed using methods described here.A general scheme is shown in FIG. 7. Particles that bind to human breastcancer cell line MDA-MB-231 and mouse pancreatic cell line panc02 havebeen selected. In each case, enrichment of cell binding particles wasobserved after 4 rounds of selection and clones taken from the 6^(th)round were shown to have cell line specific binding. Strikingly, aclearly sequence motif was apparent among the clones that bound topanc02. The particles do not bind to several other epithelial derivedcell lines tested.

FIGS. 57A and 57B summarizes the results of the selection of pancreaticcancer cell line panc02 targeting particles. The mouse pancreatic linespanc02 was panned with a single module DNA nanoparticle library. Afterthe 3^(rd) and 4^(th) round, the selected pool was fluorescently labeledand tested on the target cells by flow cytometry (FIG. 57A). A shiftindicating enrichment of binding clones was observed. After the 5^(th)and 6^(th) round, clones were generated from the selected pool andsequenced (TABLE 6). 10 of the 12 sequenced clones contained a specificsequence motif: AATGGGGCG (SEQ ID NO:12). In two of the clones the motifappears in the same frame (C45 and C58). Two independent clones for eachwe recovered with the sequence of clone 40 and 46.

TABLE 6 SEQ ID Clone Sequence NO: C33TGCTTTTTGGAACTCCTGCTAGATGATGGAATATCA 02AGGCTGATTAAACGGGGCGTTTCCTGAAATGTATTA CTTGTTGAGGTGACGTTGAGTTGGATCC C39TGCTTTTTGGAACTCCTGCTTAGCAGTAAGAAAGTA 03CAATGGGGCGATAACCCCAATCATGACTAAAAATAT GATTCGGAGGTGACGTTGAGTTGGATCC C40TGCTTTTTGGAACTCCTGCTAAACAAAAGAGGATTG 04TATGGGGCGTATCAGTTCGACTATCTGGTAGAGCAA AGAAAAGTGGTGACGTTGAGTTGGATCC C43TGCTTTTTGGAACTCCTGCTAACCGGAAGTTCGTAT 05GGCCAAAGCTGATTAAAACGGGGCGTTTACACAAGG TGTATGTGGGTGACGTTGAGTTGGATCC C44TGCTTTTTGGAACTCCTGCTATAGCTGAAGGATATT 06GGATCGGGGAGTTTTGGATTTACGATTTAGATTTGTTATGTTCTCTTGGGTGACGTTGGGATCCGGTGACGT TGAGTTGGATCC C45TGCTTTTTGGAACTCCTGCTGAATAGAGAACAACTA 07AATTCTGCAATGATGTTGCGTAGTGACTAANGATCA AATGGGGCGGTGACGTTGAGTTGGATCC C46TGCTTTTTGGAACTCCTGCTGATCAGGTTATAAAGC 08GTTAATAGCTTAATAAAACTTGAAAGGTAATAAATG GGGCGTCTGGTGACGTTGAGTTGGATCC C58TGCTTTTTGGAACTCCTGCTAAAGAGTACGAGGTAG 09AAATATGAGAAACTTTAAATTTGTCCAGCAGATCCT AATGGGGCGGTGACGTTGAGTTGGATCC C21TGCTTTTTGGAACTCCTGCTAGACGTTAGATGTATC 10TGACCTTACGACTTCAACTTCCTTCTAAATCTGCCC ACAACGATGGTGACGTTGAGTTGGATCC C50TGCTTTTTGGAACTCCTGCTCAACTTGTGTCCTCTT 11GAAAGAGTCGGTCATACCTATAAGAATACTTTTATA CAGCCAAAGGTGACGTTGAGTTGGATCC

The clones that contain the AATGGGGCG (SEQ ID NO: 12) motif bindspecifically to panc02, whereas the clones lacking the motif (C21 andC50) do not (FIG. 57B). In the experiment shown, the four clones thatshow a fluorescent shift in the left panel all contain the motif whereasthe clones without the motif are no better than controls. No differenceis seen against other epithelial cell lines.

Selecting for T Cell Binding DNA-NP

DNA-NP that bind to an implantable mouse tumor cell line (panc02) areused. Therefore, DNA-NP that bind the T-cell binding motif also, areselected. Three approaches are used. (1) Primary mouse T cells obtainedfrom PBMCs by negative selection are screened. Binding particles arechecked for binding to human T cells. (2) A mixture of human and mouse Tcells is screened, with the notion that a crossreactive particles wouldhave a selective advantage during the screening. Candidate particles arechecked against both mouse and human T cells. (3) Alternate mouse andhuman will be alternated in each round of screening.

Once a particular screening is performed for 6-8 cycles, the pool ofparticles present at that stage is analyzed by incorporating fluorescentnucleotides and checking the binding by flow cytometry. If thepopulation looks like it has enriched for binding, individual candidateparticles are recovered by subcloning the PCR amplified templates intobacteria. Candidates are sequenced and regenerated by asymmetric PCR/RCAfor further testing as particles. The specificity of binding clones isanalyzed by incubating the particles with PBMCs and anti-CD3 antibodies.The particle fluorescence should be confined to the CD3+ population.

Construct and Validate Hybrid Particle that Bind to T Cells andPancreatic Cancer Cell.

The templates for the T cell and panc02 binding motifs are ligatedtogether. Adding an additional module to a cell binding particle doesnot significantly reduce the cell binding. At least five uniquecombinations of panc02 and T cell binding motifs are produced and testedfor binding to both cell types independently by flow cytometry.T-cell/panc02 cell crosslinking is evaluated in several ways. First,varying numbers of particles with an equal mixture of both cell typesare incubated together. High concentrations of particles will lead towholesale crosslinking and essential agglutinate the cells are expected,whereas lower concentrations will form primarily heterocellular dimers.The former is evaluated by microscopy and the later by flow cytometryusing differently labeled anti-CD3 and anti-EpCAM antibodies todistinguish hetero and homocellular aggregates.

In addition, direct cell lysis during co-culture of the panc02 with Tcells from the same mouse strain (C57BL/6) from which the line wasderived, using either LDH or chromium release assays is evaluated. Thestoicheometry of particle to target cells is optimized by titrating theparticles and the relative number of cells, and the time course for celllysis determined. In addition, the effect, if any, of particle size isevaluated, by producing particles of ˜50, 100, and 200 nm as measured bydynamic light scattering. With this panel of assays, which hybrid DNA-NPcombinations are most potent is determined.

Evaluate the Effects of Bi-Specific DNA-NP on Tumor Growth andMetastasis.

Hybrid particles are analyzed for circulating half-life in normal mice,as a function of particle size. In addition, particle accumulation inliver, spleen, and lymph nodes are measured. In all cases, the particlescan be easily quantitated by real-time PCR, with the same primers usedto amplify the particles during the selection. Indeed, since eachparticle consists of many copies of the repeated sequence, singleparticle sensitive is achievable. Some of these methods allow thede-selection of any particle that has exceptionally rapid clearance, andestablish the optimal size for subsequent tumor studies.

Example 16 Targeting Dendritic Cells with DNA-Nanoparticles

Dendritic cell (DC)-based immune therapy for cancer has met with somesuccess using ex vivo approaches of injecting antigen-pulsed mature DCsinto patients. However, in vitro generation of DCs is costly,cumbersome, and difficult to standardize. Thus, activation of DCs insitu is an attractive approach but requires agents that can bothspecifically target and activate DC. DNA-NP library technology isdescribed herein that can select cell specific binding NP made solely ofsingle stranded DNA. Using such techenology, DNA-NP have been identifiedthat bind specifically to DCs, are taken up, induce Ca²⁺ flux, and IL-6secretion by DCs, and can act as vaccine adjuvants in mice. Theseresults show a DC targeting molecule that also carries intrinsicadjuvant properties. This example illustrates targeted DNA-NPs that bindto and stimulate DCs, and cause immune activation and prevent or retardtumor growth.

Production, Characterization, and Purification of DNA Nanoparticles

DNA nanoparticles were produced by methods described herein. Highdiversity libraries of DNA-NP were generated using methods describedherein, and DNA-NP that bind specifically to DCs were selected throughan iterative screening and re-amplification.

DC binding DNA-NP was verified using separate batches of particles andsynthesizing particles from both the original clone (PCR from bacteriacolonies harboring the clone, followed by asymmetric PCR with a 5′phosphate on only the desired primer for subsequent strand ligation androlling circle amplification (RCA) or from a synthetic oligonucleotidetemplate with the same sequence. The stability of particles kept at −20°C. and 4° C. for several weeks; no loss of activity was observed.

DC Binding DNA-NP Activate DC

DC binding DNA-NP cause DC activation as measured by cytokine secretion,and Ca²⁺ signaling, and surface marker expression. IL-6 secretion is acommonly used indicator that DC have matured into immune activatingcells, though a full cytokine secretion profile is ultimately desirableto confirm this point. DCs exposed to several of the DC binding DNA-NPssecrete IL-6, IL-12, and TNF-alpha. In addition, Ca²⁺ flux 20 secondsafter DC were exposed to DC binding DNA NP was detected, but not afterexposure to control DNA-NP.

An immunization study was carried out in which DNA-NP were mixed withovalbumin and injected s.c. into mice, boosted two weeks later, andanalyzed a week after the final boost for antibody responses by serumIgG titers. Robust antibody responses were seen in all mice immunizedwith DC binding DNA-NP even though the dose is much lower than typicalimmunization protocols with CpG oligonucleotides (ODN) (FIG. 57). Sinceour particles are single molecules made up of contameric repeats(n=˜300) of the complement of the template circle from which they areproduced, the dose can be expressed as either the number of particles(68 fmol), or as the number of complement repeats (20 pmol).

Screening DNA-NP that Activate DC

Five 5 DNA-NP that bind to DC were identified. All 5 DC binding DNA-NPsare compared for their ability to activate myeloid (CD11c+) bonemarrow-derived DCs (BM-DCs) in vitro, as these are known to functionsimilarly to human monocyte-derived DCs. BM-DCs will be generated(Telusma G, et al. Dendritic cell activating peptides induce distinctcytokine profiles. Int Immunol. 2006; 18:1563-1573). DC activation andmaturation is characterized by altered surface expression ofcharacteristic molecules, production of large amounts of cytokines andenhanced T cell stimulatory capacity. DC stimulatory capacity of theDC-binding DNA-NPs is evaluated in three ways: 1) their ability to alterthe expression of surface molecules on immature DCs that are classicallyup or down regulated upon maturation; 2) their ability to inducesecretion of inflammatory cytokines, and finally 3) their ability tomature DCs into effective antigen presenting cells that can activateantigen-specific T cells. The particles are ranked according to theiractivity in these assays.

In vivo selection of ligands that bind to cells or soluble proteins hasbeen well established, for example, with phage displayed peptidelibraries. In vivo selections have two significant advantages. The firstis that the selection is being performed in the very same environmentthat the ultimate product will be used. The second is that the rest ofthe animal acts as a subtractive substrate that will remove anynon-specific particles.

In vivo selections are performed with DNA-NP by injecting the DNAparticle library subcutaneously and recovering the draining lymph nodesseveral hours later. The lymph nodes are treated with collagenase tocreate single cell suspensions, and the CD11c+DCs are isolated bymagnetic bead separation. Subsequently the particle recovery,re-amplification, and ligation will be as described herein.

Injection of DNA-NP into Tumors to Activate Tumor Infiltrating DC

All in vivo experiments are conducted in a transplantable mouse model ofmelanoma using the mouse melanoma cell line B16-OVA that expresseschicken ovalbumin (OVA), which serves as a tumor marker to monitorimmune responses. When injected s.c. into C57/BL6 mice, B16-OVA producesa local tumor growth.

C57/BL6 mice (n=5 per group) are inoculated with 5×10⁵ B16 cells s.c.Once the tumors reach 3-5 mm in size, they receive intra-tumoralinjection of: 50 μl of PBS, DC binding DNA-NP, or a control DNA-NP.DNA-NPs are injected at 1 and 10 μg/ml (˜10¹⁰ and 10¹¹ particles)suspended in PBS. 24-48 hours later the mice will be sacrificed and thetumor, draining lymph nodes, blood, liver, and spleen are collected.Histology is performed on the tumor and the number of infiltratinglymphocytes compared (CD3+ and CD11c+) to controls. Single cellsuspensions are made by treating the tissue with collagenase and tumorinfiltrating DCs are analyzed for the expression levels ofco-stimulatory and adhesion molecules, e.g. CD80, CD86, MHC class II,CD40, by flow cytometry. The expression of IL-12, IFNγ, TNF-α and RANTESis determined by intracellular staining combined with surface CD11c andanalyzed by flow cytometry.

Long term tumor monitoring is performed. Groups of mice (n=5) areinoculated with tumor and injected with DNA-NP or controls. The micereceive 5-10 daily injections of DC-targeting DNA-NPs, controlnon-targeting DNA-NPs or PBS. Mice are monitored for tumor size a set ofcalipers: A×B²/2 (A=long axis, B=short axis) daily until the lastinjection and then bi-weekly over a period of 20 days. After 20 days orif the tumors reach 1.5 cm in diameter, whichever occurs first, mice aresacrificed. The spleen, liver, and kidney will be weighed and tissueanalysis will be performed by our molecular pathology core. If the pilotstudy indicates potential tumor retardation or regression in the micethat received the DNA-NP without overt toxicity then a larger study willbe designed in coordination with the biostatistics core.

Immunization with DNA-NP and Model Tumor Antigens

Co-injection of the most potent DNA-NPs with tumor antigen is likely tolead to the induction of anti-tumor immune response. OVA serves a modeltumor antigen for which tool to measure immune responses have beendeveloped and thus allows one to easily monitor the potency and type ofinduced immune response.

Immunizations: Groups of C57BL/6 mice (n=10) receive s.c. injections ofOVA/PBS (as negative control), OVA/IFA (positive control), or OVA/CpG(positive control), and 3 different doses of OVA/DNA-NPs (1-100μg/mouse), that demonstrate DC activation. Two to three weeks after theprimary immunization, the animals receive a second “booster”immunization performed exactly as the first injections. Blood isobtained from mice at three time points: before immunization for baseantibody levels, before the booster immunization and 1-2 weeks after thesecond “booster” immunization. Plasma IgG and IgM levels specific forthe injected antigen is measured by direct ELISA using plates coatedwith antigen=OVA protein. The antibody results are determined inarbitrary units against an ELISA reference serum in order to reliablecompare results obtained on different days. The type of immune responseis evaluated by measuring the subclass antibody concentrations. Inmouse, the production of IgG2a is recognized as characteristic of a Th1response, whereas the production of IgG1 is characteristic of a Th2response. Therefore, the assessment of the type of immune response isdone by measuring IgG1, IgG2a and IgG2b levels by ELISA. The ratio ofIgG2a/IgG1 antibody titers is used as indicator of Th bias.

The in vivo induced T cell responses is detected in vitro using thefollowing assays: (1) Proliferation assays are performed by addingOVA₂₅₇₋₂₆₄ peptides (to stimulate CD8 T cells) and OVA₃₂₃₋₃₃₉ (tostimulate CD4 T cells), PBS/no peptide (negative control), or ConA(positive control) to splenocytes from immunized mice which contain Tcells and antigen presenting cells, and measuring the uptake of[³H]-thymidine after 4 d. (2) A Th2 response is also characterized bythe secretion of Th2 type cytokines, such as IL-4, IL-5, whereas a Th1type response is characterized by the secretion of IL-2 and IFN-γ⁴⁶⁻⁴⁷.To measure type of T cell responses, splenocytes are set up as describedherein using phorbol myristate acetate (PMA) and soluble anti-CD3, sinceConA is not a very potent stimulus for Th2 cytokines. After 24 h theculture supernatants are assessed for IL-4, IL-2, IL-5, IL-10, TGF-α andIFN-γ levels by ELISA. (3) IFN-γ ELISPOT and intracellular flowcytometry assays (using brefeldin A to prevent leakage of the cytokinesfor the latter) for IL-4, IL-2 and IFN-γ are used to measure the numberof cytokine secreting T cells and double labeling for CD4 and CD8 todetect the type of T cells responding. (4) To measure the generation offunctional CTL responses splenocytes are cultured in medium only andre-stimulated for with mitomycin C-treated (50 μg/ml) or irradiatedB16-OVA cells and IL-2 for 6 days. As positive control splenocytes arestimulated with concavalin A (5 μg/ml). Expanded splenocytes arecultured with B16-OVA target cells and B16 (=negative control targetcells), using a standard 4 h LDH assay.

Tumor Rejection Studies

Conditions that gave the strongest immune responses are used for tumorrejection studies. Prophylactic setting: 7 days after the finalimmunization C57/BL6 mice (10 per group) are challenged with 5×10⁵ B16cells s.c. and tumor growth are monitored as described herein.Therapeutic setting: C57/BL6 mice are inoculated with 5×10⁵ B16 cellss.c. Once the tumors reach 3 mm in size, groups of mice (n=20) receives.c. immunizations of OVA protein mixed with: PBS, or the DNA-NPsconditions that induced strongest immune responses. Half the mice fromeach group (n=10) are sacrificed 7 days after the final immunization toanalyze immune responses and the other half are monitored for tumorprogression.

Pharmacodynamics and Toxicity of DNA-NPs In Vivo

Immunization experiments provide an opportunity to gain insight into thein vivo distribution and half life of the DNA-NPs, as well as anyassociated toxicity. Organs and blood are recovered from the sacrificedanimals and tissue extracts prepared. DNA-NP are quantified by real timePCR to evaluate the biodistribution and circulating levels of theparticles.

A powerful feature of the DNA-NP methods described herein is that thetemplate sequence from which the particles are generated can be easilymanipulated. One or more synthetic oligonucleotides can be used to buildthe template and beyond a minimum size of 60-80 bases, the RCA reactionproceeds equally well on templates regardless of size. Therefore, oncediscrete particle sequences are identified a hybrid template can beprepared by coupling the templates at the ligation step. Certain DCbinding particles that show activity can be combined to further enhancetheir potency.

All references cited herein, including but not limited to published andunpublished applications, patents, and literature references, areincorporated herein by reference in their entirety and are hereby made apart of this specification. To the extent publications and patents orpatent applications incorporated by reference contradict the disclosurecontained in the specification, the specification is intended tosupersede and/or take precedence over any such contradictory material.

The term “comprising” as used herein is synonymous with “including,”“containing,” or “characterized by,” and is inclusive or open-ended anddoes not exclude additional, unrecited elements or method steps.

All numbers expressing quantities of ingredients, reaction conditions,and so forth used in the specification are to be understood as beingmodified in all instances by the term “about.” Accordingly, unlessindicated to the contrary, the numerical parameters set forth herein areapproximations that may vary depending upon the desired propertiessought to be obtained. At the very least, and not as an attempt to limitthe application of the doctrine of equivalents to the scope of anyclaims in any application claiming priority to the present application,each numerical parameter should be construed in light of the number ofsignificant digits and ordinary rounding approaches.

The above description discloses several methods and materials of thepresent invention. This invention is susceptible to modifications in themethods and materials, as well as alterations in the fabrication methodsand equipment. Such modifications will become apparent to those skilledin the art from a consideration of this disclosure or practice of theinvention disclosed herein. Consequently, it is not intended that thisinvention be limited to the specific embodiments disclosed herein, butthat it cover all modifications and alternatives coming within the truescope and spirit of the invention.

1.-61. (canceled)
 62. A method of making a nanoparticle comprising:contacting a circular single-stranded nucleic acid template with anucleic acid polymerase, wherein said template includes a modulesequence which binds to a target molecule, wherein the module sequencein monovalent form has low affinity for the target molecule and inmultivalent form binds to the target molecule with a high avidity; andamplifying said template with said polymerase to produce saidnanoparticle, wherein said nanoparticle comprises a continuous strand ofnucleic acid comprising a concatamer of said module sequence.
 63. Themethod of claim 62, wherein the target molecule is bound to a surface.64. The method of claim 62, wherein said nucleic acid template is DNA.65. The method of claim 62, wherein said nucleic acid polymerase is astrand displacing polymerase.
 66. The method of claim 62, wherein saidamplifying has a duration of more than 1 minute.
 67. The method of claim62, further comprising circularizing a linear nucleic acid template toproduce said circular nucleic acid template.
 68. A non-naturallyoccurring nanoparticle made according to the method of claim
 62. 69. Thenanoparticle of claim 68, wherein said nucleic acid comprises DNA,wherein said DNA is more than 100 kb in length.
 70. The nanoparticle ofclaim 68, wherein said DNA comprises a sequence encoding a sequenceselected from a siRNA, reporter gene, therapeutic protein, and CpGsequence.
 71. The nanoparticle of claim 68, further comprising a nucleicacid intercalating drug.
 72. The nanoparticle of claim 68, furthercomprising an oligonucleotide-linked entity selected from the groupconsisting of an aptamer, drug, peptide, and siRNA.
 73. A liposomecomprising the nanoparticle of claim
 68. 74. A pharmaceuticalcomposition comprising the nanoparticle of claim
 68. 75. A method oftreating cancer comprising administering the pharmaceutical compositionof claim 74 to a subject in need thereof.
 76. A method for identifyingnanoparticles comprising a module sequence capable of binding to atarget molecule with high avidity comprising: generating a library ofnanoparticles comprising putative module sequences using the method ofclaim 62; contacting said library to a target molecule; and selectingfor a nanoparticle that binds said target molecule, wherein the modulesequence in monovalent form has low affinity for the target molecule andin multivalent form binds to the target molecule with a high avidity.77. A non-naturally occurring nanoparticle comprising a single-strandnucleic acid comprising a continuous strand of nucleic acid comprising aconcatameric module sequence which binds to a target molecule, whereinthe module sequence in monovalent form has low affinity for the targetmolecule and in multivalent form binds to the target molecule with ahigh avidity.
 78. The nanoparticle of claim 77, wherein the targetmolecule is bound on the surface.
 79. The nanoparticle of claim 77,wherein said nucleic acid comprises DNA, wherein said DNA is more than100 kb in length.
 80. The nanoparticle of claim 79, wherein said DNAcomprises a sequence encoding a sequence selected from a siRNA, reportergene, therapeutic protein, and CpG sequence.
 81. The nanoparticle ofclaim 77, further comprising a nucleic acid intercalating drug.
 82. Thenanoparticle of claim 77, further comprising an oligonucleotide-linkedentity selected from the group consisting of an aptamer, drug, peptide,and siRNA.
 83. A liposome comprising the nanoparticle of claim
 77. 84. Apharmaceutical composition comprising the nanoparticle of claim 77
 85. Amethod of treating cancer comprising administering the pharmaceuticalcomposition of claim 84 to a subject in need thereof.
 86. A method ofidentifying a target comprising: contacting said target with thenanoparticle of claim 77, wherein said module sequence selectively bindsto said target; and identifying binding of said module sequence to saidtarget.
 87. A library of nanoparticles comprising at least twopopulations of nanoparticles, wherein said each of said at least twopopulations comprise nanoparticles comprising a single-strand nucleicacid comprising a continuous strand of nucleic acid comprising aconcatamer of at least one different module sequence which binds to atarget molecule bound, wherein the module sequence in monovalent formhas low affinity for the target molecule and in multivalent form bindsto the target molecule with a high avidity.